community_model_pooled_12.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import cobra\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Community modeling\n",
    "\n",
    "In this notebook we will implement a method to create community models of two or more species specific metabolic models using cobrapy."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Growth:  0.2823653925322476\n",
      "Growth:  2.558694612613393\n"
     ]
    }
   ],
   "source": [
    "model_DP = cobra.io.read_sbml_model(\"models/consistent_DP_SNM.xml\")\n",
    "model_SA = cobra.io.read_sbml_model(\"models/consistent_iYS854_SNM.xml\")\n",
    "print(\"Growth: \", model_DP.slim_optimize())\n",
    "print(\"Growth: \", model_SA.slim_optimize())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Compound</th>\n",
       "      <th>BiGG</th>\n",
       "      <th>ModelSeed</th>\n",
       "      <th>KEGG</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Alanine</td>\n",
       "      <td>ala__L</td>\n",
       "      <td>cpd00035</td>\n",
       "      <td>C00041</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Arginine</td>\n",
       "      <td>arg__L</td>\n",
       "      <td>cpd00051</td>\n",
       "      <td>C00062</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Cysteine</td>\n",
       "      <td>cys__L</td>\n",
       "      <td>cpd00084</td>\n",
       "      <td>C00097</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Glutamic acid</td>\n",
       "      <td>glu__L</td>\n",
       "      <td>cpd00023</td>\n",
       "      <td>C00025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Glycine</td>\n",
       "      <td>gly</td>\n",
       "      <td>cpd00033</td>\n",
       "      <td>C00037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Histidine</td>\n",
       "      <td>his__L</td>\n",
       "      <td>cpd00119</td>\n",
       "      <td>C00135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Leucine</td>\n",
       "      <td>leu__L</td>\n",
       "      <td>cpd00107</td>\n",
       "      <td>C00123</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Lysine</td>\n",
       "      <td>lys__L</td>\n",
       "      <td>cpd00039</td>\n",
       "      <td>C00047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Ornithine</td>\n",
       "      <td>orn</td>\n",
       "      <td>cpd00064</td>\n",
       "      <td>C00077</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Phenylalanine</td>\n",
       "      <td>phe__L</td>\n",
       "      <td>cpd00066</td>\n",
       "      <td>C00079</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Proline</td>\n",
       "      <td>pro__L</td>\n",
       "      <td>cpd00129</td>\n",
       "      <td>C00148</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Serine</td>\n",
       "      <td>ser__L</td>\n",
       "      <td>cpd00054</td>\n",
       "      <td>C00065</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Threonine</td>\n",
       "      <td>thr__L</td>\n",
       "      <td>cpd00161</td>\n",
       "      <td>C00188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Tryptophane</td>\n",
       "      <td>trp__L</td>\n",
       "      <td>cpd00065</td>\n",
       "      <td>C00078</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Valine</td>\n",
       "      <td>val__L</td>\n",
       "      <td>cpd00156</td>\n",
       "      <td>C00183</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>citric acid</td>\n",
       "      <td>cit</td>\n",
       "      <td>cpd00137</td>\n",
       "      <td>C00158</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Fumaric acid</td>\n",
       "      <td>fum</td>\n",
       "      <td>cpd00106</td>\n",
       "      <td>C00122</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>maleic acid</td>\n",
       "      <td>male</td>\n",
       "      <td>cpd00996</td>\n",
       "      <td>C01384</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>pyruvic acid</td>\n",
       "      <td>pyr</td>\n",
       "      <td>cpd00020</td>\n",
       "      <td>C00022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>succinic acid</td>\n",
       "      <td>succ</td>\n",
       "      <td>cpd00036</td>\n",
       "      <td>C00042</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>glucose</td>\n",
       "      <td>glc__D</td>\n",
       "      <td>cpd00027</td>\n",
       "      <td>C00031</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>Urea</td>\n",
       "      <td>urea</td>\n",
       "      <td>cpd00073</td>\n",
       "      <td>C00086</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Sodium</td>\n",
       "      <td>na1</td>\n",
       "      <td>cpd00971</td>\n",
       "      <td>C01330</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Chloride</td>\n",
       "      <td>cl</td>\n",
       "      <td>cpd00099</td>\n",
       "      <td>C00698</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Potassium</td>\n",
       "      <td>k</td>\n",
       "      <td>cpd00205</td>\n",
       "      <td>C00238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Phosphate</td>\n",
       "      <td>pi</td>\n",
       "      <td>cpd00009</td>\n",
       "      <td>C00009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Magnesium</td>\n",
       "      <td>mg2</td>\n",
       "      <td>cpd00254</td>\n",
       "      <td>C00305</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Sulphate</td>\n",
       "      <td>so4</td>\n",
       "      <td>cpd00048</td>\n",
       "      <td>C00059</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>2,2'-Bipyridine</td>\n",
       "      <td>NaN</td>\n",
       "      <td>cpd25442</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>Calcium</td>\n",
       "      <td>ca2</td>\n",
       "      <td>cpd00063</td>\n",
       "      <td>C00076</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>ZnCl2</td>\n",
       "      <td>zn2</td>\n",
       "      <td>cpd00034</td>\n",
       "      <td>C00038</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>MnCl2</td>\n",
       "      <td>mn2</td>\n",
       "      <td>cpd00030</td>\n",
       "      <td>C00034</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>H3BO3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>cpd09225</td>\n",
       "      <td>C12486</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>CoCl2</td>\n",
       "      <td>cobalt2</td>\n",
       "      <td>cpd00149</td>\n",
       "      <td>C00175</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>CuCl2</td>\n",
       "      <td>cu2</td>\n",
       "      <td>cpd00058</td>\n",
       "      <td>C00070</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>NiCl2</td>\n",
       "      <td>ni2</td>\n",
       "      <td>cpd00244</td>\n",
       "      <td>C00291</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>MoNa2O4</td>\n",
       "      <td>mobd</td>\n",
       "      <td>cpd11574</td>\n",
       "      <td>C06232</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>Cyanocobalamine</td>\n",
       "      <td>adocbl</td>\n",
       "      <td>cpd01826</td>\n",
       "      <td>C02823</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>p-Aminobenzoic acid</td>\n",
       "      <td>4abz</td>\n",
       "      <td>cpd00443</td>\n",
       "      <td>C00568</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>Biotin</td>\n",
       "      <td>btn</td>\n",
       "      <td>cpd00104</td>\n",
       "      <td>C00120</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>Nicotinic acid</td>\n",
       "      <td>nac</td>\n",
       "      <td>cpd00218</td>\n",
       "      <td>C00253</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>Ca-D-Pantothenic acid</td>\n",
       "      <td>pnto__R</td>\n",
       "      <td>cpd00644</td>\n",
       "      <td>C00864</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>Pyridoxamine-2HCl</td>\n",
       "      <td>pydam</td>\n",
       "      <td>cpd00419</td>\n",
       "      <td>C00534</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>Thiamine-dichloride</td>\n",
       "      <td>thm</td>\n",
       "      <td>cpd00305</td>\n",
       "      <td>C00378</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>Riboflavin</td>\n",
       "      <td>ribflv</td>\n",
       "      <td>cpd00220</td>\n",
       "      <td>C00255</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>Oxygen</td>\n",
       "      <td>o2</td>\n",
       "      <td>cpd00007</td>\n",
       "      <td>C00007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>Fe3+</td>\n",
       "      <td>fe2</td>\n",
       "      <td>cpd10516</td>\n",
       "      <td>C14819</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>Water</td>\n",
       "      <td>h2o</td>\n",
       "      <td>cpd00001</td>\n",
       "      <td>C00001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>Co2</td>\n",
       "      <td>co2</td>\n",
       "      <td>cpd00011</td>\n",
       "      <td>C00011</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 Compound     BiGG ModelSeed    KEGG\n",
       "0                 Alanine   ala__L  cpd00035  C00041\n",
       "1                Arginine   arg__L  cpd00051  C00062\n",
       "2                Cysteine   cys__L  cpd00084  C00097\n",
       "3           Glutamic acid   glu__L  cpd00023  C00025\n",
       "4                 Glycine      gly  cpd00033  C00037\n",
       "5               Histidine   his__L  cpd00119  C00135\n",
       "6                 Leucine   leu__L  cpd00107  C00123\n",
       "7                  Lysine   lys__L  cpd00039  C00047\n",
       "8               Ornithine      orn  cpd00064  C00077\n",
       "9           Phenylalanine   phe__L  cpd00066  C00079\n",
       "10                Proline   pro__L  cpd00129  C00148\n",
       "11                 Serine   ser__L  cpd00054  C00065\n",
       "12              Threonine   thr__L  cpd00161  C00188\n",
       "13            Tryptophane   trp__L  cpd00065  C00078\n",
       "14                 Valine   val__L  cpd00156  C00183\n",
       "15            citric acid      cit  cpd00137  C00158\n",
       "16           Fumaric acid      fum  cpd00106  C00122\n",
       "17            maleic acid     male  cpd00996  C01384\n",
       "18           pyruvic acid      pyr  cpd00020  C00022\n",
       "19          succinic acid     succ  cpd00036  C00042\n",
       "20                glucose   glc__D  cpd00027  C00031\n",
       "21                   Urea     urea  cpd00073  C00086\n",
       "22                 Sodium      na1  cpd00971  C01330\n",
       "23               Chloride       cl  cpd00099  C00698\n",
       "24              Potassium        k  cpd00205  C00238\n",
       "25              Phosphate       pi  cpd00009  C00009\n",
       "26              Magnesium      mg2  cpd00254  C00305\n",
       "27               Sulphate      so4  cpd00048  C00059\n",
       "28        2,2'-Bipyridine      NaN  cpd25442     NaN\n",
       "29                Calcium      ca2  cpd00063  C00076\n",
       "30                  ZnCl2      zn2  cpd00034  C00038\n",
       "31                  MnCl2      mn2  cpd00030  C00034\n",
       "32                  H3BO3      NaN  cpd09225  C12486\n",
       "33                  CoCl2  cobalt2  cpd00149  C00175\n",
       "34                  CuCl2      cu2  cpd00058  C00070\n",
       "35                  NiCl2      ni2  cpd00244  C00291\n",
       "36                MoNa2O4     mobd  cpd11574  C06232\n",
       "37        Cyanocobalamine   adocbl  cpd01826  C02823\n",
       "38    p-Aminobenzoic acid     4abz  cpd00443  C00568\n",
       "39                 Biotin      btn  cpd00104  C00120\n",
       "40         Nicotinic acid      nac  cpd00218  C00253\n",
       "41  Ca-D-Pantothenic acid  pnto__R  cpd00644  C00864\n",
       "42      Pyridoxamine-2HCl    pydam  cpd00419  C00534\n",
       "43    Thiamine-dichloride      thm  cpd00305  C00378\n",
       "44             Riboflavin   ribflv  cpd00220  C00255\n",
       "45                 Oxygen       o2  cpd00007  C00007\n",
       "46                   Fe3+      fe2  cpd10516  C14819\n",
       "47                  Water      h2o  cpd00001  C00001\n",
       "48                    Co2      co2  cpd00011  C00011"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "snm3 = pd.read_csv(\"SNM3.csv\", sep =\";\")\n",
    "snm3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "BIOMASS_DP = \"Growth\" \n",
    "BIOMASS_SA = \"BIOMASS_iYS_wild_type\"\n",
    "models = [model_DP.copy(), model_SA.copy()]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2) Bag of reactions community model\n",
    "\n",
    "Before we created compartments to seperate both organisms. Now we will only consider a bag of reactions, throwing all reactions into one bucket."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_bag_of_react_model(models, biomass_functions, weights=\"auto\"):\n",
    "    # Bag of words model\n",
    "    model = model_DP + model_SA\n",
    "\n",
    "    if weights == \"auto\":\n",
    "        biomass = []\n",
    "        for model_i in models:\n",
    "            biomass.append(model_i.slim_optimize())\n",
    "        max_biomass = np.max(biomass)\n",
    "        weights = [max_biomass/g for g in biomass]\n",
    "    \n",
    "    # Set objective as sum of growth\n",
    "    objective = []\n",
    "    for i, growth in enumerate(biomass_functions):\n",
    "        v_i = weights[i] * model.reactions.get_by_id(growth).flux_expression\n",
    "        objective.append(v_i)\n",
    "    model.objective = sum(objective)\n",
    "    return model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Ignoring reaction 'ACALD' since it already exists.\n",
      "Ignoring reaction 'ACALDt' since it already exists.\n",
      "Ignoring reaction '3OAS140' since it already exists.\n",
      "Ignoring reaction '3OAS60' since it already exists.\n",
      "Ignoring reaction 'ACCOAC' since it already exists.\n",
      "Ignoring reaction '5DOAN' since it already exists.\n",
      "Ignoring reaction '6PHBG' since it already exists.\n",
      "Ignoring reaction '6PHBG2' since it already exists.\n",
      "Ignoring reaction 'ACGS' since it already exists.\n",
      "Ignoring reaction 'ACKr' since it already exists.\n",
      "Ignoring reaction '3HAD100' since it already exists.\n",
      "Ignoring reaction '3HAD120' since it already exists.\n",
      "Ignoring reaction '3HAD140' since it already exists.\n",
      "Ignoring reaction 'ACACT1r' since it already exists.\n",
      "Ignoring reaction '3HAD60' since it already exists.\n",
      "Ignoring reaction 'ACM6PH' since it already exists.\n",
      "Ignoring reaction '3OAR100' since it already exists.\n",
      "Ignoring reaction '3OAR140' since it already exists.\n",
      "Ignoring reaction '3OAR60' since it already exists.\n",
      "Ignoring reaction '3OAS100' since it already exists.\n",
      "Ignoring reaction 'ACOATA' since it already exists.\n",
      "Ignoring reaction 'ACODA' since it already exists.\n",
      "Ignoring reaction 'AKGDH' since it already exists.\n",
      "Ignoring reaction 'ALAALAr' since it already exists.\n",
      "Ignoring reaction 'ALAD_L' since it already exists.\n",
      "Ignoring reaction 'ALAR' since it already exists.\n",
      "Ignoring reaction 'ALCD19' since it already exists.\n",
      "Ignoring reaction 'ALCD2ir' since it already exists.\n",
      "Ignoring reaction 'ARGDr' since it already exists.\n",
      "Ignoring reaction 'ADK1' since it already exists.\n",
      "Ignoring reaction 'AMANAPEr' since it already exists.\n",
      "Ignoring reaction 'ADK3' since it already exists.\n",
      "Ignoring reaction 'ADK4' since it already exists.\n",
      "Ignoring reaction 'ADKd' since it already exists.\n",
      "Ignoring reaction 'ADNUC' since it already exists.\n",
      "Ignoring reaction 'ADPT' since it already exists.\n",
      "Ignoring reaction 'ATPM' since it already exists.\n",
      "Ignoring reaction 'ADSL1r' since it already exists.\n",
      "Ignoring reaction 'ADSL2r' since it already exists.\n",
      "Ignoring reaction 'ADSS' since it already exists.\n",
      "Ignoring reaction 'AGDC' since it already exists.\n",
      "Ignoring reaction 'CYTD' since it already exists.\n",
      "Ignoring reaction 'DHPS2' since it already exists.\n",
      "Ignoring reaction 'CYTK1' since it already exists.\n",
      "Ignoring reaction 'CYTK2' since it already exists.\n",
      "Ignoring reaction 'Cut1' since it already exists.\n",
      "Ignoring reaction 'DADK' since it already exists.\n",
      "Ignoring reaction 'DATPHs' since it already exists.\n",
      "Ignoring reaction 'CO2t' since it already exists.\n",
      "Ignoring reaction 'COabc' since it already exists.\n",
      "Ignoring reaction 'DCYTD' since it already exists.\n",
      "Ignoring reaction 'DMATT' since it already exists.\n",
      "Ignoring reaction 'CTPS1' since it already exists.\n",
      "Ignoring reaction 'CTPS2' since it already exists.\n",
      "Ignoring reaction 'DGK1' since it already exists.\n",
      "Ignoring reaction 'DHAPT' since it already exists.\n",
      "Ignoring reaction 'DHORTS' since it already exists.\n",
      "Ignoring reaction 'DHFR' since it already exists.\n",
      "Ignoring reaction 'DHFS' since it already exists.\n",
      "Ignoring reaction 'DHNPA2r' since it already exists.\n",
      "Ignoring reaction 'DNMPPA' since it already exists.\n",
      "Ignoring reaction 'DHORDi' since it already exists.\n",
      "Ignoring reaction 'DNTPPA' since it already exists.\n",
      "Ignoring reaction 'EX_acald_e' since it already exists.\n",
      "Ignoring reaction 'DPMVD' since it already exists.\n",
      "Ignoring reaction 'DPR' since it already exists.\n",
      "Ignoring reaction 'EX_h2o_e' since it already exists.\n",
      "Ignoring reaction 'EX_arg__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_h_e' since it already exists.\n",
      "Ignoring reaction 'EX_his__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_ile__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_k_e' since it already exists.\n",
      "Ignoring reaction 'EX_lac__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_leu__L_e' since it already exists.\n",
      "Ignoring reaction 'DRPA' since it already exists.\n",
      "Ignoring reaction 'EX_lys__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_cl_e' since it already exists.\n",
      "Ignoring reaction 'EX_co2_e' since it already exists.\n",
      "Ignoring reaction 'EX_cys__L_e' since it already exists.\n",
      "Ignoring reaction 'DTMPK' since it already exists.\n",
      "Ignoring reaction 'EX_met__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_mg2_e' since it already exists.\n",
      "Ignoring reaction 'EX_mn2_e' since it already exists.\n",
      "Ignoring reaction 'EX_na1_e' since it already exists.\n",
      "Ignoring reaction 'EX_fe2_e' since it already exists.\n",
      "Ignoring reaction 'EX_nac_e' since it already exists.\n",
      "Ignoring reaction 'EX_nh4_e' since it already exists.\n",
      "Ignoring reaction 'EX_o2_e' since it already exists.\n",
      "Ignoring reaction 'EX_orn_e' since it already exists.\n",
      "Ignoring reaction 'EX_phe__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_pi_e' since it already exists.\n",
      "Ignoring reaction 'D_LACt2' since it already exists.\n",
      "Ignoring reaction 'EX_glc__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_rib__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_glu__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_ribflv_e' since it already exists.\n",
      "Ignoring reaction 'EX_so4_e' since it already exists.\n",
      "Ignoring reaction 'EX_trp__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_tyr__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_thm_e' since it already exists.\n",
      "Ignoring reaction 'EX_ura_e' since it already exists.\n",
      "Ignoring reaction 'EX_val__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_zn2_e' since it already exists.\n",
      "Ignoring reaction 'ENO' since it already exists.\n",
      "Ignoring reaction 'G3PD2' since it already exists.\n",
      "Ignoring reaction 'FBA' since it already exists.\n",
      "Ignoring reaction 'FBA2' since it already exists.\n",
      "Ignoring reaction 'FBA3' since it already exists.\n",
      "Ignoring reaction 'G6PBDH' since it already exists.\n",
      "Ignoring reaction 'G6PDA' since it already exists.\n",
      "Ignoring reaction 'FE2abc' since it already exists.\n",
      "Ignoring reaction 'G6PI' since it already exists.\n",
      "Ignoring reaction 'G6PP' since it already exists.\n",
      "Ignoring reaction 'GCALDD' since it already exists.\n",
      "Ignoring reaction 'GF6PTA' since it already exists.\n",
      "Ignoring reaction 'GGTT' since it already exists.\n",
      "Ignoring reaction 'GLUR' since it already exists.\n",
      "Ignoring reaction 'FRTT' since it already exists.\n",
      "Ignoring reaction 'FRUK' since it already exists.\n",
      "Ignoring reaction 'GHMT2r' since it already exists.\n",
      "Ignoring reaction 'GK1' since it already exists.\n",
      "Ignoring reaction 'FTHFLi' since it already exists.\n",
      "Ignoring reaction 'FUM' since it already exists.\n",
      "Ignoring reaction 'G1PACT' since it already exists.\n",
      "Ignoring reaction 'G1SAT' since it already exists.\n",
      "Ignoring reaction 'GLUTRR' since it already exists.\n",
      "Ignoring reaction 'GLCpts' since it already exists.\n",
      "Ignoring reaction 'GLNS' since it already exists.\n",
      "Ignoring reaction 'GLUabc' since it already exists.\n",
      "Ignoring reaction 'GLUt4' since it already exists.\n",
      "Ignoring reaction 'GLUPRT' since it already exists.\n",
      "Ignoring reaction 'GLYAT' since it already exists.\n",
      "Ignoring reaction 'ILETA' since it already exists.\n",
      "Ignoring reaction 'GUAPRT' since it already exists.\n",
      "Ignoring reaction 'H2Ot' since it already exists.\n",
      "Ignoring reaction 'HCO3E' since it already exists.\n",
      "Ignoring reaction 'ILEt2r' since it already exists.\n",
      "Ignoring reaction 'IMPC' since it already exists.\n",
      "Ignoring reaction 'IMPD' since it already exists.\n",
      "Ignoring reaction 'INSH' since it already exists.\n",
      "Ignoring reaction 'IPDDI' since it already exists.\n",
      "Ignoring reaction 'HEXTT' since it already exists.\n",
      "Ignoring reaction 'HISabc' since it already exists.\n",
      "Ignoring reaction 'KAS14' since it already exists.\n",
      "Ignoring reaction 'KAS15' since it already exists.\n",
      "Ignoring reaction 'KAS16' since it already exists.\n",
      "Ignoring reaction 'HMBS' since it already exists.\n",
      "Ignoring reaction 'HPYRRx' since it already exists.\n",
      "Ignoring reaction 'Kt2r' since it already exists.\n",
      "Ignoring reaction 'LDH_L' since it already exists.\n",
      "Ignoring reaction 'HXPRT' since it already exists.\n",
      "Ignoring reaction 'LEUt2r' since it already exists.\n",
      "Ignoring reaction 'LGTHL' since it already exists.\n",
      "Ignoring reaction 'GLYOX' since it already exists.\n",
      "Ignoring reaction 'MGt5' since it already exists.\n",
      "Ignoring reaction 'MACPD' since it already exists.\n",
      "Ignoring reaction 'MMSAD3' since it already exists.\n",
      "Ignoring reaction 'MNabc' since it already exists.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Ignoring reaction 'MOHMT' since it already exists.\n",
      "Ignoring reaction 'MTHFC' since it already exists.\n",
      "Ignoring reaction 'MTHFD' since it already exists.\n",
      "Ignoring reaction 'MCOATA' since it already exists.\n",
      "Ignoring reaction 'ME1' since it already exists.\n",
      "Ignoring reaction 'NACt' since it already exists.\n",
      "Ignoring reaction 'ME2' since it already exists.\n",
      "Ignoring reaction 'METAT' since it already exists.\n",
      "Ignoring reaction 'METS' since it already exists.\n",
      "Ignoring reaction 'NAt3_1' since it already exists.\n",
      "Ignoring reaction 'METabc' since it already exists.\n",
      "Ignoring reaction 'NDPK2' since it already exists.\n",
      "Ignoring reaction 'MEVK2' since it already exists.\n",
      "Ignoring reaction 'MEVK3' since it already exists.\n",
      "Ignoring reaction 'MEVK4' since it already exists.\n",
      "Ignoring reaction 'NDPK4' since it already exists.\n",
      "Ignoring reaction 'NNAM' since it already exists.\n",
      "Ignoring reaction 'NNATr' since it already exists.\n",
      "Ignoring reaction 'GMPR' since it already exists.\n",
      "Ignoring reaction 'GMPS2' since it already exists.\n",
      "Ignoring reaction 'PC' since it already exists.\n",
      "Ignoring reaction 'GND' since it already exists.\n",
      "Ignoring reaction 'NTD10' since it already exists.\n",
      "Ignoring reaction 'PDH' since it already exists.\n",
      "Ignoring reaction 'NTD2' since it already exists.\n",
      "Ignoring reaction 'NTD3' since it already exists.\n",
      "Ignoring reaction 'PDHbr' since it already exists.\n",
      "Ignoring reaction 'PDHcr' since it already exists.\n",
      "Ignoring reaction 'NTD4' since it already exists.\n",
      "Ignoring reaction 'NTD5' since it already exists.\n",
      "Ignoring reaction 'NTD6' since it already exists.\n",
      "Ignoring reaction 'NTD7' since it already exists.\n",
      "Ignoring reaction 'NTD8' since it already exists.\n",
      "Ignoring reaction 'NTD9' since it already exists.\n",
      "Ignoring reaction 'PFK' since it already exists.\n",
      "Ignoring reaction 'PFK_4' since it already exists.\n",
      "Ignoring reaction 'PFL' since it already exists.\n",
      "Ignoring reaction 'PGAMT' since it already exists.\n",
      "Ignoring reaction 'PGI' since it already exists.\n",
      "Ignoring reaction 'PGK' since it already exists.\n",
      "Ignoring reaction 'PGL' since it already exists.\n",
      "Ignoring reaction 'PGM' since it already exists.\n",
      "Ignoring reaction 'PGMT' since it already exists.\n",
      "Ignoring reaction 'O2t' since it already exists.\n",
      "Ignoring reaction 'PHETA1' since it already exists.\n",
      "Ignoring reaction 'GRTT' since it already exists.\n",
      "Ignoring reaction 'OIVD1r' since it already exists.\n",
      "Ignoring reaction 'OIVD2' since it already exists.\n",
      "Ignoring reaction 'OIVD3' since it already exists.\n",
      "Ignoring reaction 'OMPDC' since it already exists.\n",
      "Ignoring reaction 'ORNTAC' since it already exists.\n",
      "Ignoring reaction 'ORPT' since it already exists.\n",
      "Ignoring reaction 'GTHOr' since it already exists.\n",
      "Ignoring reaction 'PMEVK' since it already exists.\n",
      "Ignoring reaction 'PMPK' since it already exists.\n",
      "Ignoring reaction 'GTHPi' since it already exists.\n",
      "Ignoring reaction 'PYK' since it already exists.\n",
      "Ignoring reaction 'SDPDS' since it already exists.\n",
      "Ignoring reaction 'RBK' since it already exists.\n",
      "Ignoring reaction 'RIBFLVt2' since it already exists.\n",
      "Ignoring reaction 'PPA' since it already exists.\n",
      "Ignoring reaction 'PPBNGS' since it already exists.\n",
      "Ignoring reaction 'PPCDC' since it already exists.\n",
      "Ignoring reaction 'PPM' since it already exists.\n",
      "Ignoring reaction 'PPM2' since it already exists.\n",
      "Ignoring reaction 'RIBabc1' since it already exists.\n",
      "Ignoring reaction 'RNDR1' since it already exists.\n",
      "Ignoring reaction 'SDPTA' since it already exists.\n",
      "Ignoring reaction 'RNDR2' since it already exists.\n",
      "Ignoring reaction 'RNDR3' since it already exists.\n",
      "Ignoring reaction 'RNDR4' since it already exists.\n",
      "Ignoring reaction 'RNTR1' since it already exists.\n",
      "Ignoring reaction 'RNTR2' since it already exists.\n",
      "Ignoring reaction 'RNTR3' since it already exists.\n",
      "Ignoring reaction 'RNTR4' since it already exists.\n",
      "Ignoring reaction 'PPTT' since it already exists.\n",
      "Ignoring reaction 'PRAGSr' since it already exists.\n",
      "Ignoring reaction 'PRAIS_1' since it already exists.\n",
      "Ignoring reaction 'PRASCSi' since it already exists.\n",
      "Ignoring reaction 'PRFGS' since it already exists.\n",
      "Ignoring reaction 'RPE' since it already exists.\n",
      "Ignoring reaction 'RPI' since it already exists.\n",
      "Ignoring reaction 'PRPPS' since it already exists.\n",
      "Ignoring reaction 'PTAr' since it already exists.\n",
      "Ignoring reaction 'PTPATi' since it already exists.\n",
      "Ignoring reaction 'THMabc' since it already exists.\n",
      "Ignoring reaction 'THRD_L' since it already exists.\n",
      "Ignoring reaction 'TKT1' since it already exists.\n",
      "Ignoring reaction 'TKT2' since it already exists.\n",
      "Ignoring reaction 'UMPK' since it already exists.\n",
      "Ignoring reaction 'UPP3S' since it already exists.\n",
      "Ignoring reaction 'UPPDC1' since it already exists.\n",
      "Ignoring reaction 'TMDS' since it already exists.\n",
      "Ignoring reaction 'TMPPP' since it already exists.\n",
      "Ignoring reaction 'TPI' since it already exists.\n",
      "Ignoring reaction 'TRDR' since it already exists.\n",
      "Ignoring reaction 'UPPRT' since it already exists.\n",
      "Ignoring reaction 'URAt2' since it already exists.\n",
      "Ignoring reaction 'URIDK2r' since it already exists.\n",
      "Ignoring reaction 'TRPt2r' since it already exists.\n",
      "Ignoring reaction 'VALTA' since it already exists.\n",
      "Ignoring reaction 'VALt2r' since it already exists.\n",
      "Ignoring reaction 'TYRt2r' since it already exists.\n",
      "Ignoring reaction 'UAMAGS' since it already exists.\n",
      "Ignoring reaction 'UAMAS' since it already exists.\n",
      "Ignoring reaction 'UAPGR' since it already exists.\n",
      "Ignoring reaction 'UDCPDP' since it already exists.\n",
      "Ignoring reaction 'XPPT' since it already exists.\n",
      "Ignoring reaction 'XTSNH' since it already exists.\n",
      "Ignoring reaction 'ZNabc' since it already exists.\n",
      "Ignoring reaction 'TALA' since it already exists.\n",
      "Ignoring reaction 'THDPS' since it already exists.\n",
      "Ignoring reaction 'EX_glyclt_e' since it already exists.\n",
      "Ignoring reaction 'THIORDXi' since it already exists.\n",
      "Ignoring reaction 'UAG2EMA' since it already exists.\n"
     ]
    }
   ],
   "source": [
    "model1_1 = create_bag_of_react_model([model_DP,model_SA],[BIOMASS_DP, BIOMASS_SA], weights=[1.,1.])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MBR Weights 1:1:  5.359696176521698\n",
      "SA growth: 5.010482140405494\n",
      "DP growth: 0.3492140361162044\n"
     ]
    }
   ],
   "source": [
    "print(\"MBR Weights 1:1: \", model1_1.slim_optimize())\n",
    "print(\"SA growth: \" + str(model1_1.reactions.get_by_id(BIOMASS_SA).flux))\n",
    "print(\"DP growth: \" + str(model1_1.reactions.get_by_id(BIOMASS_DP).flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SA growth: 5.010482140405494\n",
      "DP growth: 0.3492140361162044\n"
     ]
    }
   ],
   "source": [
    "opt = model1_1.optimize()\n",
    "print(\"SA growth: \" + str(model1_1.reactions.get_by_id(BIOMASS_SA).flux))\n",
    "print(\"DP growth: \" + str(model1_1.reactions.get_by_id(BIOMASS_DP).flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Ignoring reaction 'ACALD' since it already exists.\n",
      "Ignoring reaction 'ACALDt' since it already exists.\n",
      "Ignoring reaction '3OAS140' since it already exists.\n",
      "Ignoring reaction '3OAS60' since it already exists.\n",
      "Ignoring reaction 'ACCOAC' since it already exists.\n",
      "Ignoring reaction '5DOAN' since it already exists.\n",
      "Ignoring reaction '6PHBG' since it already exists.\n",
      "Ignoring reaction '6PHBG2' since it already exists.\n",
      "Ignoring reaction 'ACGS' since it already exists.\n",
      "Ignoring reaction 'ACKr' since it already exists.\n",
      "Ignoring reaction '3HAD100' since it already exists.\n",
      "Ignoring reaction '3HAD120' since it already exists.\n",
      "Ignoring reaction '3HAD140' since it already exists.\n",
      "Ignoring reaction 'ACACT1r' since it already exists.\n",
      "Ignoring reaction '3HAD60' since it already exists.\n",
      "Ignoring reaction 'ACM6PH' since it already exists.\n",
      "Ignoring reaction '3OAR100' since it already exists.\n",
      "Ignoring reaction '3OAR140' since it already exists.\n",
      "Ignoring reaction '3OAR60' since it already exists.\n",
      "Ignoring reaction '3OAS100' since it already exists.\n",
      "Ignoring reaction 'ACOATA' since it already exists.\n",
      "Ignoring reaction 'ACODA' since it already exists.\n",
      "Ignoring reaction 'AKGDH' since it already exists.\n",
      "Ignoring reaction 'ALAALAr' since it already exists.\n",
      "Ignoring reaction 'ALAD_L' since it already exists.\n",
      "Ignoring reaction 'ALAR' since it already exists.\n",
      "Ignoring reaction 'ALCD19' since it already exists.\n",
      "Ignoring reaction 'ALCD2ir' since it already exists.\n",
      "Ignoring reaction 'ARGDr' since it already exists.\n",
      "Ignoring reaction 'ADK1' since it already exists.\n",
      "Ignoring reaction 'AMANAPEr' since it already exists.\n",
      "Ignoring reaction 'ADK3' since it already exists.\n",
      "Ignoring reaction 'ADK4' since it already exists.\n",
      "Ignoring reaction 'ADKd' since it already exists.\n",
      "Ignoring reaction 'ADNUC' since it already exists.\n",
      "Ignoring reaction 'ADPT' since it already exists.\n",
      "Ignoring reaction 'ATPM' since it already exists.\n",
      "Ignoring reaction 'ADSL1r' since it already exists.\n",
      "Ignoring reaction 'ADSL2r' since it already exists.\n",
      "Ignoring reaction 'ADSS' since it already exists.\n",
      "Ignoring reaction 'AGDC' since it already exists.\n",
      "Ignoring reaction 'CYTD' since it already exists.\n",
      "Ignoring reaction 'DHPS2' since it already exists.\n",
      "Ignoring reaction 'CYTK1' since it already exists.\n",
      "Ignoring reaction 'CYTK2' since it already exists.\n",
      "Ignoring reaction 'Cut1' since it already exists.\n",
      "Ignoring reaction 'DADK' since it already exists.\n",
      "Ignoring reaction 'DATPHs' since it already exists.\n",
      "Ignoring reaction 'CO2t' since it already exists.\n",
      "Ignoring reaction 'COabc' since it already exists.\n",
      "Ignoring reaction 'DCYTD' since it already exists.\n",
      "Ignoring reaction 'DMATT' since it already exists.\n",
      "Ignoring reaction 'CTPS1' since it already exists.\n",
      "Ignoring reaction 'CTPS2' since it already exists.\n",
      "Ignoring reaction 'DGK1' since it already exists.\n",
      "Ignoring reaction 'DHAPT' since it already exists.\n",
      "Ignoring reaction 'DHORTS' since it already exists.\n",
      "Ignoring reaction 'DHFR' since it already exists.\n",
      "Ignoring reaction 'DHFS' since it already exists.\n",
      "Ignoring reaction 'DHNPA2r' since it already exists.\n",
      "Ignoring reaction 'DNMPPA' since it already exists.\n",
      "Ignoring reaction 'DHORDi' since it already exists.\n",
      "Ignoring reaction 'DNTPPA' since it already exists.\n",
      "Ignoring reaction 'EX_acald_e' since it already exists.\n",
      "Ignoring reaction 'DPMVD' since it already exists.\n",
      "Ignoring reaction 'DPR' since it already exists.\n",
      "Ignoring reaction 'EX_h2o_e' since it already exists.\n",
      "Ignoring reaction 'EX_arg__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_h_e' since it already exists.\n",
      "Ignoring reaction 'EX_his__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_ile__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_k_e' since it already exists.\n",
      "Ignoring reaction 'EX_lac__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_leu__L_e' since it already exists.\n",
      "Ignoring reaction 'DRPA' since it already exists.\n",
      "Ignoring reaction 'EX_lys__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_cl_e' since it already exists.\n",
      "Ignoring reaction 'EX_co2_e' since it already exists.\n",
      "Ignoring reaction 'EX_cys__L_e' since it already exists.\n",
      "Ignoring reaction 'DTMPK' since it already exists.\n",
      "Ignoring reaction 'EX_met__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_mg2_e' since it already exists.\n",
      "Ignoring reaction 'EX_mn2_e' since it already exists.\n",
      "Ignoring reaction 'EX_na1_e' since it already exists.\n",
      "Ignoring reaction 'EX_fe2_e' since it already exists.\n",
      "Ignoring reaction 'EX_nac_e' since it already exists.\n",
      "Ignoring reaction 'EX_nh4_e' since it already exists.\n",
      "Ignoring reaction 'EX_o2_e' since it already exists.\n",
      "Ignoring reaction 'EX_orn_e' since it already exists.\n",
      "Ignoring reaction 'EX_phe__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_pi_e' since it already exists.\n",
      "Ignoring reaction 'D_LACt2' since it already exists.\n",
      "Ignoring reaction 'EX_glc__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_rib__D_e' since it already exists.\n",
      "Ignoring reaction 'EX_glu__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_ribflv_e' since it already exists.\n",
      "Ignoring reaction 'EX_so4_e' since it already exists.\n",
      "Ignoring reaction 'EX_trp__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_tyr__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_thm_e' since it already exists.\n",
      "Ignoring reaction 'EX_ura_e' since it already exists.\n",
      "Ignoring reaction 'EX_val__L_e' since it already exists.\n",
      "Ignoring reaction 'EX_zn2_e' since it already exists.\n",
      "Ignoring reaction 'ENO' since it already exists.\n",
      "Ignoring reaction 'G3PD2' since it already exists.\n",
      "Ignoring reaction 'FBA' since it already exists.\n",
      "Ignoring reaction 'FBA2' since it already exists.\n",
      "Ignoring reaction 'FBA3' since it already exists.\n",
      "Ignoring reaction 'G6PBDH' since it already exists.\n",
      "Ignoring reaction 'G6PDA' since it already exists.\n",
      "Ignoring reaction 'FE2abc' since it already exists.\n",
      "Ignoring reaction 'G6PI' since it already exists.\n",
      "Ignoring reaction 'G6PP' since it already exists.\n",
      "Ignoring reaction 'GCALDD' since it already exists.\n",
      "Ignoring reaction 'GF6PTA' since it already exists.\n",
      "Ignoring reaction 'GGTT' since it already exists.\n",
      "Ignoring reaction 'GLUR' since it already exists.\n",
      "Ignoring reaction 'FRTT' since it already exists.\n",
      "Ignoring reaction 'FRUK' since it already exists.\n",
      "Ignoring reaction 'GHMT2r' since it already exists.\n",
      "Ignoring reaction 'GK1' since it already exists.\n",
      "Ignoring reaction 'FTHFLi' since it already exists.\n",
      "Ignoring reaction 'FUM' since it already exists.\n",
      "Ignoring reaction 'G1PACT' since it already exists.\n",
      "Ignoring reaction 'G1SAT' since it already exists.\n",
      "Ignoring reaction 'GLUTRR' since it already exists.\n",
      "Ignoring reaction 'GLCpts' since it already exists.\n",
      "Ignoring reaction 'GLNS' since it already exists.\n",
      "Ignoring reaction 'GLUabc' since it already exists.\n",
      "Ignoring reaction 'GLUt4' since it already exists.\n",
      "Ignoring reaction 'GLUPRT' since it already exists.\n",
      "Ignoring reaction 'GLYAT' since it already exists.\n",
      "Ignoring reaction 'ILETA' since it already exists.\n",
      "Ignoring reaction 'GUAPRT' since it already exists.\n",
      "Ignoring reaction 'H2Ot' since it already exists.\n",
      "Ignoring reaction 'HCO3E' since it already exists.\n",
      "Ignoring reaction 'ILEt2r' since it already exists.\n",
      "Ignoring reaction 'IMPC' since it already exists.\n",
      "Ignoring reaction 'IMPD' since it already exists.\n",
      "Ignoring reaction 'INSH' since it already exists.\n",
      "Ignoring reaction 'IPDDI' since it already exists.\n",
      "Ignoring reaction 'HEXTT' since it already exists.\n",
      "Ignoring reaction 'HISabc' since it already exists.\n",
      "Ignoring reaction 'KAS14' since it already exists.\n",
      "Ignoring reaction 'KAS15' since it already exists.\n",
      "Ignoring reaction 'KAS16' since it already exists.\n",
      "Ignoring reaction 'HMBS' since it already exists.\n",
      "Ignoring reaction 'HPYRRx' since it already exists.\n",
      "Ignoring reaction 'Kt2r' since it already exists.\n",
      "Ignoring reaction 'LDH_L' since it already exists.\n",
      "Ignoring reaction 'HXPRT' since it already exists.\n",
      "Ignoring reaction 'LEUt2r' since it already exists.\n",
      "Ignoring reaction 'LGTHL' since it already exists.\n",
      "Ignoring reaction 'GLYOX' since it already exists.\n",
      "Ignoring reaction 'MGt5' since it already exists.\n",
      "Ignoring reaction 'MACPD' since it already exists.\n",
      "Ignoring reaction 'MMSAD3' since it already exists.\n",
      "Ignoring reaction 'MNabc' since it already exists.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Ignoring reaction 'MOHMT' since it already exists.\n",
      "Ignoring reaction 'MTHFC' since it already exists.\n",
      "Ignoring reaction 'MTHFD' since it already exists.\n",
      "Ignoring reaction 'MCOATA' since it already exists.\n",
      "Ignoring reaction 'ME1' since it already exists.\n",
      "Ignoring reaction 'NACt' since it already exists.\n",
      "Ignoring reaction 'ME2' since it already exists.\n",
      "Ignoring reaction 'METAT' since it already exists.\n",
      "Ignoring reaction 'METS' since it already exists.\n",
      "Ignoring reaction 'NAt3_1' since it already exists.\n",
      "Ignoring reaction 'METabc' since it already exists.\n",
      "Ignoring reaction 'NDPK2' since it already exists.\n",
      "Ignoring reaction 'MEVK2' since it already exists.\n",
      "Ignoring reaction 'MEVK3' since it already exists.\n",
      "Ignoring reaction 'MEVK4' since it already exists.\n",
      "Ignoring reaction 'NDPK4' since it already exists.\n",
      "Ignoring reaction 'NNAM' since it already exists.\n",
      "Ignoring reaction 'NNATr' since it already exists.\n",
      "Ignoring reaction 'GMPR' since it already exists.\n",
      "Ignoring reaction 'GMPS2' since it already exists.\n",
      "Ignoring reaction 'PC' since it already exists.\n",
      "Ignoring reaction 'GND' since it already exists.\n",
      "Ignoring reaction 'NTD10' since it already exists.\n",
      "Ignoring reaction 'PDH' since it already exists.\n",
      "Ignoring reaction 'NTD2' since it already exists.\n",
      "Ignoring reaction 'NTD3' since it already exists.\n",
      "Ignoring reaction 'PDHbr' since it already exists.\n",
      "Ignoring reaction 'PDHcr' since it already exists.\n",
      "Ignoring reaction 'NTD4' since it already exists.\n",
      "Ignoring reaction 'NTD5' since it already exists.\n",
      "Ignoring reaction 'NTD6' since it already exists.\n",
      "Ignoring reaction 'NTD7' since it already exists.\n",
      "Ignoring reaction 'NTD8' since it already exists.\n",
      "Ignoring reaction 'NTD9' since it already exists.\n",
      "Ignoring reaction 'PFK' since it already exists.\n",
      "Ignoring reaction 'PFK_4' since it already exists.\n",
      "Ignoring reaction 'PFL' since it already exists.\n",
      "Ignoring reaction 'PGAMT' since it already exists.\n",
      "Ignoring reaction 'PGI' since it already exists.\n",
      "Ignoring reaction 'PGK' since it already exists.\n",
      "Ignoring reaction 'PGL' since it already exists.\n",
      "Ignoring reaction 'PGM' since it already exists.\n",
      "Ignoring reaction 'PGMT' since it already exists.\n",
      "Ignoring reaction 'O2t' since it already exists.\n",
      "Ignoring reaction 'PHETA1' since it already exists.\n",
      "Ignoring reaction 'GRTT' since it already exists.\n",
      "Ignoring reaction 'OIVD1r' since it already exists.\n",
      "Ignoring reaction 'OIVD2' since it already exists.\n",
      "Ignoring reaction 'OIVD3' since it already exists.\n",
      "Ignoring reaction 'OMPDC' since it already exists.\n",
      "Ignoring reaction 'ORNTAC' since it already exists.\n",
      "Ignoring reaction 'ORPT' since it already exists.\n",
      "Ignoring reaction 'GTHOr' since it already exists.\n",
      "Ignoring reaction 'PMEVK' since it already exists.\n",
      "Ignoring reaction 'PMPK' since it already exists.\n",
      "Ignoring reaction 'GTHPi' since it already exists.\n",
      "Ignoring reaction 'PYK' since it already exists.\n",
      "Ignoring reaction 'SDPDS' since it already exists.\n",
      "Ignoring reaction 'RBK' since it already exists.\n",
      "Ignoring reaction 'RIBFLVt2' since it already exists.\n",
      "Ignoring reaction 'PPA' since it already exists.\n",
      "Ignoring reaction 'PPBNGS' since it already exists.\n",
      "Ignoring reaction 'PPCDC' since it already exists.\n",
      "Ignoring reaction 'PPM' since it already exists.\n",
      "Ignoring reaction 'PPM2' since it already exists.\n",
      "Ignoring reaction 'RIBabc1' since it already exists.\n",
      "Ignoring reaction 'RNDR1' since it already exists.\n",
      "Ignoring reaction 'SDPTA' since it already exists.\n",
      "Ignoring reaction 'RNDR2' since it already exists.\n",
      "Ignoring reaction 'RNDR3' since it already exists.\n",
      "Ignoring reaction 'RNDR4' since it already exists.\n",
      "Ignoring reaction 'RNTR1' since it already exists.\n",
      "Ignoring reaction 'RNTR2' since it already exists.\n",
      "Ignoring reaction 'RNTR3' since it already exists.\n",
      "Ignoring reaction 'RNTR4' since it already exists.\n",
      "Ignoring reaction 'PPTT' since it already exists.\n",
      "Ignoring reaction 'PRAGSr' since it already exists.\n",
      "Ignoring reaction 'PRAIS_1' since it already exists.\n",
      "Ignoring reaction 'PRASCSi' since it already exists.\n",
      "Ignoring reaction 'PRFGS' since it already exists.\n",
      "Ignoring reaction 'RPE' since it already exists.\n",
      "Ignoring reaction 'RPI' since it already exists.\n",
      "Ignoring reaction 'PRPPS' since it already exists.\n",
      "Ignoring reaction 'PTAr' since it already exists.\n",
      "Ignoring reaction 'PTPATi' since it already exists.\n",
      "Ignoring reaction 'THMabc' since it already exists.\n",
      "Ignoring reaction 'THRD_L' since it already exists.\n",
      "Ignoring reaction 'TKT1' since it already exists.\n",
      "Ignoring reaction 'TKT2' since it already exists.\n",
      "Ignoring reaction 'UMPK' since it already exists.\n",
      "Ignoring reaction 'UPP3S' since it already exists.\n",
      "Ignoring reaction 'UPPDC1' since it already exists.\n",
      "Ignoring reaction 'TMDS' since it already exists.\n",
      "Ignoring reaction 'TMPPP' since it already exists.\n",
      "Ignoring reaction 'TPI' since it already exists.\n",
      "Ignoring reaction 'TRDR' since it already exists.\n",
      "Ignoring reaction 'UPPRT' since it already exists.\n",
      "Ignoring reaction 'URAt2' since it already exists.\n",
      "Ignoring reaction 'URIDK2r' since it already exists.\n",
      "Ignoring reaction 'TRPt2r' since it already exists.\n",
      "Ignoring reaction 'VALTA' since it already exists.\n",
      "Ignoring reaction 'VALt2r' since it already exists.\n",
      "Ignoring reaction 'TYRt2r' since it already exists.\n",
      "Ignoring reaction 'UAMAGS' since it already exists.\n",
      "Ignoring reaction 'UAMAS' since it already exists.\n",
      "Ignoring reaction 'UAPGR' since it already exists.\n",
      "Ignoring reaction 'UDCPDP' since it already exists.\n",
      "Ignoring reaction 'XPPT' since it already exists.\n",
      "Ignoring reaction 'XTSNH' since it already exists.\n",
      "Ignoring reaction 'ZNabc' since it already exists.\n",
      "Ignoring reaction 'TALA' since it already exists.\n",
      "Ignoring reaction 'THDPS' since it already exists.\n",
      "Ignoring reaction 'EX_glyclt_e' since it already exists.\n",
      "Ignoring reaction 'THIORDXi' since it already exists.\n",
      "Ignoring reaction 'UAG2EMA' since it already exists.\n"
     ]
    }
   ],
   "source": [
    "model10_1 = create_bag_of_react_model([model_DP,model_SA],[BIOMASS_DP, BIOMASS_SA], weights=[10.,1.])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SA growth: 0.0\n",
      "DP growth: 1.3402800000000015\n"
     ]
    }
   ],
   "source": [
    "opt = model10_1.optimize()\n",
    "print(\"SA growth: \" + str(model10_1.reactions.get_by_id(BIOMASS_SA).flux))\n",
    "print(\"DP growth: \" + str(model10_1.reactions.get_by_id(BIOMASS_DP).flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MBR Weights 10:1:  13.402800000000015\n",
      "SA growth: 0.0\n",
      "DP growth: 1.3402800000000015\n"
     ]
    }
   ],
   "source": [
    "print(\"MBR Weights 10:1: \", model10_1.slim_optimize())\n",
    "print(\"SA growth: \" + str(model10_1.reactions.get_by_id(BIOMASS_SA).flux))\n",
    "print(\"DP growth: \" + str(model10_1.reactions.get_by_id(BIOMASS_DP).flux))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}