community_model_SNM_weights_16.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import cobra\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "from scipy.optimize import linprog\n",
    "import scipy\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore')"
   ]
  },
  {
   "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": 2,
   "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": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "for rec in model_SA.reactions:\n",
    "    rec.lower_bound = max(rec.lower_bound, -1000)\n",
    "    rec.upper_bound = min(rec.upper_bound, 1000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\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",
       "  </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"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "snm3 = pd.read_csv(\"SNM3.csv\", sep =\";\")\n",
    "snm3.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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": [
    "## 1) Constructing of community model explicitely"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_stoichiometry_matrix(model):\n",
    "    metabolites = model.metabolites \n",
    "    reactions = model.reactions \n",
    "    S = np.zeros((len(metabolites), len(reactions)))\n",
    "    \n",
    "    met_id = dict()\n",
    "    rec_id = dict()\n",
    "    for i,reaction in enumerate(model.reactions):\n",
    "        rec_id[reaction.id] = i\n",
    "        for metabolite, stoich in reaction.metabolites.items():\n",
    "            met_id[metabolite.id] = int(metabolites.index(metabolite))\n",
    "            S[metabolites.index(metabolite), i] = stoich\n",
    "    return S, met_id, rec_id "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "class Model():\n",
    "    def __init__(self, model, biomass_function):\n",
    "        \"\"\" This is a new class of metabolic model, capable of flux balance analysis\n",
    "        Attributes:\n",
    "        models (list): CobraPy models of single organisms which will be used in construction\n",
    "        biomass_reactions (list): List of strings containing the ids for the growth reactions\n",
    "        \"\"\"\n",
    "        self.biomass_function = biomass_function\n",
    "        self.model = model\n",
    "        self.id = model.id\n",
    "        # Compute stoichimetry_matrix\n",
    "        S, met_id, rec_id = create_stoichiometry_matrix(model)\n",
    "        self.num_reactions = S.shape[1]\n",
    "        self.num_metabolites = S.shape[0]\n",
    "        self.stoichiometry_matrix = scipy.sparse.csr_matrix(S)\n",
    "        self.met_id = met_id\n",
    "        self.rec_id = rec_id \n",
    "        # Set objective\n",
    "        idx = self.rec_id[biomass_function]\n",
    "        c = np.zeros(self.num_reactions)\n",
    "        c[idx] = 1\n",
    "        self.objective_c = c\n",
    "        self.medium = model.medium\n",
    "        # Set bounds\n",
    "        self._reset_bounds()\n",
    "    \n",
    "    @property\n",
    "    def reactions(self):\n",
    "        return self.model.reactions\n",
    "    @property\n",
    "    def exchanges(self):\n",
    "        return self.model.exchanges\n",
    "    @property\n",
    "    def metabolites(self):\n",
    "        return self.model.metabolites\n",
    "\n",
    "\n",
    "    def set_medium(self, medium):\n",
    "        ex_ids = [ex.id for ex in self.exchanges]\n",
    "        new_med = {}\n",
    "        for key,val in medium.items():\n",
    "            if key in ex_ids:\n",
    "                new_med[key] = val\n",
    "        self.model.medium = new_med\n",
    "        self._reset_bounds()\n",
    "        \n",
    "    def optimize(self, disp=False):\n",
    "        sol = linprog(-self.objective_c, A_eq=self.stoichiometry_matrix, b_eq=np.zeros(self.num_metabolites), bounds=self.bounds, method=\"highs\", options={\"disp\":disp})\n",
    "        sol[\"fun\"] = -sol[\"fun\"] # As we have to minimize\n",
    "        return sol \n",
    "    \n",
    "    def slim_optimize(self, disp=False):\n",
    "        sol = self.optimize(disp=disp)\n",
    "        return sol[\"fun\"]\n",
    "\n",
    "    def summary(self):\n",
    "        sol = self.optimize()\n",
    "        flux = sol[\"x\"]\n",
    "        ex_ids = [ex.id for ex in self.exchanges]\n",
    "        fluxes = []\n",
    "        for ex in ex_ids:\n",
    "            idx = self.rec_id[ex]\n",
    "            fluxes.append(flux[idx])\n",
    "        summary_df = pd.DataFrame({\"Exchange reaction\": ex_ids, \"Flux\": fluxes})\n",
    "        summary_df.sort_values([\"Flux\"], inplace=True)\n",
    "        return summary_df\n",
    "\n",
    "    def _reset_bounds(self):\n",
    "        self.bounds = []\n",
    "        for rec in self.model.reactions:\n",
    "            self.bounds.append((rec.lower_bound, rec.upper_bound))\n",
    "\n",
    "    def __add__(self, model2):\n",
    "        \"\"\" Adding another model creates a community model \"\"\"\n",
    "        return CommunityModel([self,model2], [1.,1.])\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "class CommunityModel(Model):\n",
    "    def __init__(self, models, weight):\n",
    "        self.models = models\n",
    "        self.id = \"|\".join([model.id for model in models])\n",
    "        self.shared_exchanges = []\n",
    "        self.weight = weight\n",
    "        for model in models:\n",
    "            for rec in model.exchanges:\n",
    "                if rec.id not in self.shared_exchanges:\n",
    "                    self.shared_exchanges.append(rec.id)\n",
    "        # Create community stoichimetry matrix with shuttel reactions!\n",
    "        self._shifts = [len(self.shared_exchanges)]\n",
    "        for i,model in enumerate(models):\n",
    "            self._shifts.append(self._shifts[i] + model.num_reactions)\n",
    "        S_EX = -np.eye(self._shifts[0])\n",
    "        matrices = [S_EX] + [m.stoichiometry_matrix.todense() for m in models]\n",
    "        S = scipy.linalg.block_diag(*matrices)\n",
    "        self.num_reactions = S.shape[1]\n",
    "        self.num_metabolites = S.shape[0]\n",
    "        for i, id in enumerate(self.shared_exchanges):\n",
    "            for j,model in enumerate(models):\n",
    "                if id in model.rec_id:\n",
    "                    S[i,self._shifts[j] + model.rec_id[id]] = 1\n",
    "        self.stoichiometry_matrix = scipy.sparse.csr_matrix(S)\n",
    "        # Cretae objective:\n",
    "        self._weighted_objective(weight)\n",
    "        # Create bounds\n",
    "        self._reset_bounds()\n",
    "    \n",
    "    @property\n",
    "    def reactions(self):\n",
    "        return [model.reactions for model in self.models]\n",
    "    @property\n",
    "    def exchanges(self):\n",
    "        return self.shared_exchanges\n",
    "    @property\n",
    "    def metabolites(self):\n",
    "        return [model.metabolites for model in self.models]\n",
    "    @property\n",
    "    def medium(self):\n",
    "        medium = {}\n",
    "        for model in self.models:\n",
    "            for key,val in model.medium.items():\n",
    "                medium[key] = val\n",
    "        return medium\n",
    "\n",
    "    def _weighted_objective(self, weight):\n",
    "        self.weight = weight\n",
    "        self.objective_c = np.zeros(self._shifts[0])\n",
    "        for i,model in enumerate(self.models):\n",
    "            self.objective_c = np.append(self.objective_c, weight[i]*model.objective_c)\n",
    "    def _reset_bounds(self):\n",
    "        self.bounds = []\n",
    "        for id in self.shared_exchanges:\n",
    "            min_lower_bound = 0\n",
    "            for model in self.models:\n",
    "                if id in model.rec_id:\n",
    "                    rec = model.reactions.get_by_id(id)\n",
    "                    if rec.lower_bound < min_lower_bound:\n",
    "                        min_lower_bound = rec.lower_bound \n",
    "            self.bounds.append((min_lower_bound, 1000))\n",
    "        for model in self.models:\n",
    "            self.bounds += model.bounds\n",
    "\n",
    "    def compute_alpha_weightings(self, alpha, maxbiomass=0.1):\n",
    "        assert alpha <= 1 and alpha >= 0\n",
    "        assert len(self.models) == 2\n",
    "        alphas = np.array([alpha,1-alpha])\n",
    "        # Alpha objective...\n",
    "        c = np.zeros(self._shifts[0])\n",
    "        for i, model in enumerate(self.models):\n",
    "            c = np.append(c, model.objective_c)\n",
    "        # Biomoss constraints\n",
    "        c_mask = (c > 0)\n",
    "        A_ub = np.zeros((2,len(c)))\n",
    "        A_ub[0,c_mask] = np.array([1,0])\n",
    "        A_ub[1,c_mask] = np.array([0,1])\n",
    "        b_ub = alphas*maxbiomass\n",
    "        sol = linprog(-c, A_eq=self.stoichiometry_matrix, b_eq=np.zeros(self.num_metabolites), A_ub = A_ub, b_ub=b_ub, bounds=self.bounds, method=\"highs\")\n",
    "        fluxes = sol[\"x\"]\n",
    "        growths = fluxes[c > 0]\n",
    "        summary = self.summary(sol)\n",
    "        return growths, fluxes,summary\n",
    "\n",
    "    def set_medium(self, medium):\n",
    "        for model in self.models:\n",
    "            model.set_medium(medium)\n",
    "        self._reset_bounds()\n",
    "\n",
    "    def summary(self, sol=None):\n",
    "        if sol == None:\n",
    "            sol = self.optimize()\n",
    "        flux = sol[\"x\"]\n",
    "        ex_ids = self.shared_exchanges\n",
    "        ex_flux = flux[:len(ex_ids)]\n",
    "        df_ex = pd.DataFrame({\"Exchanges\": ex_ids, \"Flux\": ex_flux})\n",
    "        df_ex.sort_values([\"Flux\"], inplace=True)\n",
    "        for i,model in enumerate(self.models):\n",
    "            shuttel_ids = [ex.id for ex in model.exchanges]\n",
    "            id = str(model.id) + \" Shuttel Flux\"\n",
    "            df_ex[id] = 0.\n",
    "            for sh in shuttel_ids:\n",
    "                idx = model.rec_id[sh]\n",
    "                df_ex[id][ex_ids.index(sh)] = flux[self._shifts[i] +idx]\n",
    "        \n",
    "        return df_ex\n",
    "    \n",
    "    def set_weights(self, weight):\n",
    "        self._weighted_objective(weight)\n",
    "    \n",
    "    def get_model_growths(self):\n",
    "        mask = self.objective_c != 0\n",
    "        sol = self.optimize()\n",
    "        flux = sol[\"x\"]\n",
    "        return flux[mask]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Growth:  0.28236539253224774\n"
     ]
    },
    {
     "data": {
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Exchange reaction</th>\n",
       "      <th>Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>EX_o2_e</td>\n",
       "      <td>-20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>EX_cys__L_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>EX_glc__D_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>EX_h2o_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>EX_arg__L_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>EX_fum_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Exchange reaction  Flux\n",
       "32           EX_o2_e -20.0\n",
       "57       EX_cys__L_e -10.0\n",
       "1        EX_glc__D_e -10.0\n",
       "2           EX_h2o_e -10.0\n",
       "16       EX_arg__L_e -10.0\n",
       "39          EX_fum_e -10.0"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model_DP = Model(model_DP, BIOMASS_DP)\n",
    "print(\"Growth: \",model_DP.slim_optimize())\n",
    "model_DP.summary().head(6)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Growth:  2.5586946126118373\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\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>Exchange reaction</th>\n",
       "      <th>Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>EX_o2_e</td>\n",
       "      <td>-20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>EX_glc__D_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>EX_orn_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>EX_pyr_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>EX_glu__L_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>EX_ser__L_e</td>\n",
       "      <td>-10.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Exchange reaction  Flux\n",
       "42           EX_o2_e -20.0\n",
       "51       EX_glc__D_e -10.0\n",
       "43          EX_orn_e -10.0\n",
       "52          EX_pyr_e -10.0\n",
       "54       EX_glu__L_e -10.0\n",
       "56       EX_ser__L_e -10.0"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "model_SA = Model(model_SA, BIOMASS_SA)\n",
    "print(\"Growth: \",model_SA.slim_optimize())\n",
    "model_SA.summary().head(6)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Weights 1:1:  2.5586946126136296\n",
      "SA growth:  2.5586946126136296\n",
      "DP growth:  -0.0\n",
      "weights 1:10  4.294950548440156\n",
      "SA growth:  1.4712966231176634\n",
      "DP growth:  0.28236539253224924\n"
     ]
    }
   ],
   "source": [
    "# Community model\n",
    "model = model_SA + model_DP\n",
    "print(\"Weights 1:1: \", model.slim_optimize())\n",
    "growths = model.get_model_growths()\n",
    "print(\"SA growth: \", growths[0])\n",
    "print(\"DP growth: \", growths[1])\n",
    "model.set_weights([1,10])\n",
    "print(\"weights 1:10 \", model.slim_optimize())\n",
    "growths = model.get_model_growths()\n",
    "print(\"SA growth: \", growths[0])\n",
    "print(\"DP growth: \", growths[1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Investigate weighting...\n",
    "\n",
    "We will fix $\\nu_{comm} = 0.1$. That is the total biomass will be fixed to 0.1. Now we will compute for several $\\alpha \\in (0,1)$ following optimization problem:\n",
    "$$ \\max \\  \\nu_{DP} + \\nu_{SA} \\text{ subject to usuall constraints and }  \\nu_{SA} \\leq \\alpha \\cdot 0.1 \\quad  \\nu_{DP} \\leq (1-\\alpha) \\cdot 0.1$$"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "summaries = dict()\n",
    "model.set_weights([1,1])\n",
    "for alpha in [i/10 for i in range(1,10)]:\n",
    "    growths, fluxes, summary = model.compute_alpha_weightings(alpha, 0.1)\n",
    "    summaries[alpha] = summary "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_full = pd.concat(summaries, join=\"outer\", axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
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       "      <td>0.0</td>\n",
       "      <td>-0.000968</td>\n",
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      "text/plain": [
       "               0.1                                                          \\\n",
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       "110  EX_26dap__M_e -0.008716                 0.0                 -0.008716   \n",
       "\n",
       "               0.2                                                          \\\n",
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       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
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       "109       EX_ni2_e -0.002840                 0.0                 -0.002840   \n",
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       "\n",
       "               0.3            ...                 0.7  \\\n",
       "         Exchanges      Flux  ... iYS854 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000  ...                -0.0   \n",
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       "..             ...       ...  ...                 ...   \n",
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       "109       EX_ni2_e -0.002485  ...                 0.0   \n",
       "110  EX_26dap__M_e -0.006779  ...                 0.0   \n",
       "\n",
       "                                         0.8                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
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       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  1.698614         EX_s_e  1.126399                 0.0   \n",
       "109                 -0.001065       EX_ni2_e -0.000710                 0.0   \n",
       "110                 -0.002905  EX_26dap__M_e -0.001937                 0.0   \n",
       "\n",
       "                                         0.9                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  1.126399         EX_s_e  0.554184                 0.0   \n",
       "109                 -0.000710       EX_ni2_e -0.000355                 0.0   \n",
       "110                 -0.001937  EX_26dap__M_e -0.000968                 0.0   \n",
       "\n",
       "                               \n",
       "    DP_83VPs_KB5 Shuttel Flux  \n",
       "0                    0.000000  \n",
       "1                    0.000000  \n",
       "2                    0.000000  \n",
       "3                    0.000000  \n",
       "4                    0.000000  \n",
       "..                        ...  \n",
       "106                  0.000000  \n",
       "107                 -0.000000  \n",
       "108                  0.554184  \n",
       "109                 -0.000355  \n",
       "110                 -0.000968  \n",
       "\n",
       "[111 rows x 36 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_full"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_full.to_csv(\"summaries_all_alpha_weight_1_1_RM.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
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       "      <th></th>\n",
       "      <th colspan=\"4\" halign=\"left\">0.1</th>\n",
       "      <th colspan=\"4\" halign=\"left\">0.2</th>\n",
       "      <th colspan=\"2\" halign=\"left\">0.3</th>\n",
       "      <th>...</th>\n",
       "      <th colspan=\"2\" halign=\"left\">0.7</th>\n",
       "      <th colspan=\"4\" halign=\"left\">0.8</th>\n",
       "      <th colspan=\"4\" halign=\"left\">0.9</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th></th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>...</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106</th>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108</th>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>5.131905</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.131905</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>4.559690</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.559690</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>3.987475</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.698614</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>1.126399</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.126399</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>0.554184</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.554184</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.003195</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.003195</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.002840</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002840</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.002485</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.001065</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.000710</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000710</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.000355</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000355</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.008716</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.008716</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.007747</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.007747</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.006779</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002905</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.001937</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.001937</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.000968</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000968</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>111 rows × 36 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               0.1                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000                -0.0                  0.000000   \n",
       "1     EX_istfrnB_e  0.000000                -0.0                  0.000000   \n",
       "2      EX_stfrnA_e  0.000000                -0.0                  0.000000   \n",
       "3      EX_stfrnB_e  0.000000                -0.0                  0.000000   \n",
       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                  0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  5.131905                 0.0                  5.131905   \n",
       "109       EX_ni2_e -0.003195                 0.0                 -0.003195   \n",
       "110  EX_26dap__M_e -0.008716                 0.0                 -0.008716   \n",
       "\n",
       "               0.2                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000                -0.0                  0.000000   \n",
       "1     EX_istfrnB_e  0.000000                -0.0                  0.000000   \n",
       "2      EX_stfrnA_e  0.000000                -0.0                  0.000000   \n",
       "3      EX_stfrnB_e  0.000000                -0.0                  0.000000   \n",
       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                  0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  4.559690                 0.0                  4.559690   \n",
       "109       EX_ni2_e -0.002840                 0.0                 -0.002840   \n",
       "110  EX_26dap__M_e -0.007747                 0.0                 -0.007747   \n",
       "\n",
       "               0.3            ...                 0.7  \\\n",
       "         Exchanges      Flux  ... iYS854 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000  ...                -0.0   \n",
       "1     EX_istfrnB_e  0.000000  ...                -0.0   \n",
       "2      EX_stfrnA_e  0.000000  ...                -0.0   \n",
       "3      EX_stfrnB_e  0.000000  ...                -0.0   \n",
       "4          EX_ac_e -0.000000  ...                 0.0   \n",
       "..             ...       ...  ...                 ...   \n",
       "106      EX_lipa_e -0.000000  ...                 0.0   \n",
       "107     EX_pdima_e -0.000000  ...                 0.0   \n",
       "108         EX_s_e  3.987475  ...                 0.0   \n",
       "109       EX_ni2_e -0.002485  ...                 0.0   \n",
       "110  EX_26dap__M_e -0.006779  ...                 0.0   \n",
       "\n",
       "                                         0.8                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  1.698614         EX_s_e  1.126399                 0.0   \n",
       "109                 -0.001065       EX_ni2_e -0.000710                 0.0   \n",
       "110                 -0.002905  EX_26dap__M_e -0.001937                 0.0   \n",
       "\n",
       "                                         0.9                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  1.126399         EX_s_e  0.554184                 0.0   \n",
       "109                 -0.000710       EX_ni2_e -0.000355                 0.0   \n",
       "110                 -0.001937  EX_26dap__M_e -0.000968                 0.0   \n",
       "\n",
       "                               \n",
       "    DP_83VPs_KB5 Shuttel Flux  \n",
       "0                    0.000000  \n",
       "1                    0.000000  \n",
       "2                    0.000000  \n",
       "3                    0.000000  \n",
       "4                    0.000000  \n",
       "..                        ...  \n",
       "106                  0.000000  \n",
       "107                 -0.000000  \n",
       "108                  0.554184  \n",
       "109                 -0.000355  \n",
       "110                 -0.000968  \n",
       "\n",
       "[111 rows x 36 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "summaries = dict()\n",
    "model.set_weights([1,10])\n",
    "for alpha in [i/10 for i in range(1,10)]:\n",
    "    growths, fluxes, summary = model.compute_alpha_weightings(alpha, 0.1)\n",
    "    summaries[alpha] = summary \n",
    "df_full = pd.concat(summaries, join=\"outer\", axis=1)\n",
    "df_full"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_full.to_csv(\"summaries_all_alpha_weight_1_10_RM.csv\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Investigate with COMPM\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "import json\n",
    "compm_SA = json.loads(open(\"compm_SA.json\").read())\n",
    "compm_DP = json.loads(open(\"compm_DP.json\").read())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "compm = dict()\n",
    "for key, val in compm_SA.items():\n",
    "    compm[key] = val \n",
    "for key, val in compm_DP.items():\n",
    "    compm[key] = val "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.set_medium(compm)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SA growth:  2.558694612613441\n",
      "DP growth:  -9.732222301975288e-13\n"
     ]
    }
   ],
   "source": [
    "model.set_weights([1,1])\n",
    "growths = model.get_model_growths()\n",
    "print(\"SA growth: \", growths[0])\n",
    "print(\"DP growth: \", growths[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SA growth:  2.175506751508334\n",
      "DP growth:  0.07290151281852739\n"
     ]
    }
   ],
   "source": [
    "model.set_weights([1,10])\n",
    "growths = model.get_model_growths()\n",
    "print(\"SA growth: \", growths[0])\n",
    "print(\"DP growth: \", growths[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "summaries = dict()\n",
    "model.set_weights([1,1])\n",
    "for alpha in [i/10 for i in range(1,10)]:\n",
    "    growths, fluxes, summary = model.compute_alpha_weightings(alpha, 0.3)\n",
    "    summaries[alpha] = summary "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
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       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
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       "      <td>0.000000</td>\n",
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       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
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       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
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       "    <tr>\n",
       "      <th>108</th>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>8.231034</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.231034</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.870420</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7.870420</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.506030</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.855337</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>8.461639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.461639</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.529321</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7.529321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.009584</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.009584</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.008519</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.008519</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.007454</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.003195</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.002130</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002130</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.001065</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.001065</td>\n",
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       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.026147</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.026147</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.023242</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.023242</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.020337</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.008716</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.005811</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.005811</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.002905</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002905</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>111 rows × 36 columns</p>\n",
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      "text/plain": [
       "               0.1                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
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       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                 -0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  8.231034                 0.0                  8.231034   \n",
       "109       EX_ni2_e -0.009584                 0.0                 -0.009584   \n",
       "110  EX_26dap__M_e -0.026147                 0.0                 -0.026147   \n",
       "\n",
       "               0.2                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000                -0.0                  0.000000   \n",
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       "3      EX_stfrnB_e  0.000000                -0.0                  0.000000   \n",
       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                  0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  7.870420                 0.0                  7.870420   \n",
       "109       EX_ni2_e -0.008519                 0.0                 -0.008519   \n",
       "110  EX_26dap__M_e -0.023242                 0.0                 -0.023242   \n",
       "\n",
       "               0.3            ...                 0.7  \\\n",
       "         Exchanges      Flux  ... iYS854 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000  ...                -0.0   \n",
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       "..             ...       ...  ...                 ...   \n",
       "106      EX_lipa_e -0.000000  ...                 0.0   \n",
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       "108         EX_s_e  7.506030  ...                 0.0   \n",
       "109       EX_ni2_e -0.007454  ...                 0.0   \n",
       "110  EX_26dap__M_e -0.020337  ...                 0.0   \n",
       "\n",
       "                                         0.8                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  8.855337         EX_s_e  8.461639                 0.0   \n",
       "109                 -0.003195       EX_ni2_e -0.002130                 0.0   \n",
       "110                 -0.008716  EX_26dap__M_e -0.005811                 0.0   \n",
       "\n",
       "                                         0.9                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  8.461639         EX_s_e  7.529321                 0.0   \n",
       "109                 -0.002130       EX_ni2_e -0.001065                 0.0   \n",
       "110                 -0.005811  EX_26dap__M_e -0.002905                 0.0   \n",
       "\n",
       "                               \n",
       "    DP_83VPs_KB5 Shuttel Flux  \n",
       "0                    0.000000  \n",
       "1                    0.000000  \n",
       "2                    0.000000  \n",
       "3                    0.000000  \n",
       "4                    0.000000  \n",
       "..                        ...  \n",
       "106                  0.000000  \n",
       "107                 -0.000000  \n",
       "108                  7.529321  \n",
       "109                 -0.001065  \n",
       "110                 -0.002905  \n",
       "\n",
       "[111 rows x 36 columns]"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_full = pd.concat(summaries, join=\"outer\", axis=1)\n",
    "df_full"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_full.to_csv(\"summaries_all_alpha_weight_1_1_compm_RM.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
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       "      <th>Flux</th>\n",
       "      <th>...</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "      <th>Exchanges</th>\n",
       "      <th>Flux</th>\n",
       "      <th>iYS854 Shuttel Flux</th>\n",
       "      <th>DP_83VPs_KB5 Shuttel Flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_istfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnA_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_stfrnB_e</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_ac_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106</th>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>EX_lipa_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>EX_pdima_e</td>\n",
       "      <td>-0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>108</th>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>8.231034</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.231034</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.870420</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7.870420</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.506030</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.855337</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>8.461639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.461639</td>\n",
       "      <td>EX_s_e</td>\n",
       "      <td>7.529321</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7.529321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.009584</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.009584</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.008519</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.008519</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.007454</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.003195</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.002130</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002130</td>\n",
       "      <td>EX_ni2_e</td>\n",
       "      <td>-0.001065</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.001065</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>110</th>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.026147</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.026147</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.023242</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.023242</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.020337</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.008716</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.005811</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.005811</td>\n",
       "      <td>EX_26dap__M_e</td>\n",
       "      <td>-0.002905</td>\n",
       "      <td>0.0</td>\n",
       "      <td>-0.002905</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>111 rows × 36 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               0.1                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000                -0.0                  0.000000   \n",
       "1     EX_istfrnB_e  0.000000                -0.0                  0.000000   \n",
       "2      EX_stfrnA_e  0.000000                -0.0                  0.000000   \n",
       "3      EX_stfrnB_e  0.000000                -0.0                  0.000000   \n",
       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                 -0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  8.231034                 0.0                  8.231034   \n",
       "109       EX_ni2_e -0.009584                 0.0                 -0.009584   \n",
       "110  EX_26dap__M_e -0.026147                 0.0                 -0.026147   \n",
       "\n",
       "               0.2                                                          \\\n",
       "         Exchanges      Flux iYS854 Shuttel Flux DP_83VPs_KB5 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000                -0.0                  0.000000   \n",
       "1     EX_istfrnB_e  0.000000                -0.0                  0.000000   \n",
       "2      EX_stfrnA_e  0.000000                -0.0                  0.000000   \n",
       "3      EX_stfrnB_e  0.000000                -0.0                  0.000000   \n",
       "4          EX_ac_e -0.000000                 0.0                  0.000000   \n",
       "..             ...       ...                 ...                       ...   \n",
       "106      EX_lipa_e -0.000000                 0.0                  0.000000   \n",
       "107     EX_pdima_e -0.000000                 0.0                 -0.000000   \n",
       "108         EX_s_e  7.870420                 0.0                  7.870420   \n",
       "109       EX_ni2_e -0.008519                 0.0                 -0.008519   \n",
       "110  EX_26dap__M_e -0.023242                 0.0                 -0.023242   \n",
       "\n",
       "               0.3            ...                 0.7  \\\n",
       "         Exchanges      Flux  ... iYS854 Shuttel Flux   \n",
       "0     EX_istfrnA_e  0.000000  ...                -0.0   \n",
       "1     EX_istfrnB_e  0.000000  ...                -0.0   \n",
       "2      EX_stfrnA_e  0.000000  ...                -0.0   \n",
       "3      EX_stfrnB_e  0.000000  ...                -0.0   \n",
       "4          EX_ac_e -0.000000  ...                 0.0   \n",
       "..             ...       ...  ...                 ...   \n",
       "106      EX_lipa_e -0.000000  ...                 0.0   \n",
       "107     EX_pdima_e -0.000000  ...                 0.0   \n",
       "108         EX_s_e  7.506030  ...                 0.0   \n",
       "109       EX_ni2_e -0.007454  ...                 0.0   \n",
       "110  EX_26dap__M_e -0.020337  ...                 0.0   \n",
       "\n",
       "                                         0.8                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  8.855337         EX_s_e  8.461639                 0.0   \n",
       "109                 -0.003195       EX_ni2_e -0.002130                 0.0   \n",
       "110                 -0.008716  EX_26dap__M_e -0.005811                 0.0   \n",
       "\n",
       "                                         0.9                                \\\n",
       "    DP_83VPs_KB5 Shuttel Flux      Exchanges      Flux iYS854 Shuttel Flux   \n",
       "0                    0.000000   EX_istfrnA_e  0.000000                -0.0   \n",
       "1                    0.000000   EX_istfrnB_e  0.000000                -0.0   \n",
       "2                    0.000000    EX_stfrnA_e  0.000000                -0.0   \n",
       "3                    0.000000    EX_stfrnB_e  0.000000                -0.0   \n",
       "4                    0.000000        EX_ac_e -0.000000                 0.0   \n",
       "..                        ...            ...       ...                 ...   \n",
       "106                  0.000000      EX_lipa_e -0.000000                 0.0   \n",
       "107                 -0.000000     EX_pdima_e -0.000000                 0.0   \n",
       "108                  8.461639         EX_s_e  7.529321                 0.0   \n",
       "109                 -0.002130       EX_ni2_e -0.001065                 0.0   \n",
       "110                 -0.005811  EX_26dap__M_e -0.002905                 0.0   \n",
       "\n",
       "                               \n",
       "    DP_83VPs_KB5 Shuttel Flux  \n",
       "0                    0.000000  \n",
       "1                    0.000000  \n",
       "2                    0.000000  \n",
       "3                    0.000000  \n",
       "4                    0.000000  \n",
       "..                        ...  \n",
       "106                  0.000000  \n",
       "107                 -0.000000  \n",
       "108                  7.529321  \n",
       "109                 -0.001065  \n",
       "110                 -0.002905  \n",
       "\n",
       "[111 rows x 36 columns]"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "summaries = dict()\n",
    "model.set_weights([1,10])\n",
    "for alpha in [i/10 for i in range(1,10)]:\n",
    "    growths, fluxes, summary = model.compute_alpha_weightings(alpha, 0.3)\n",
    "    summaries[alpha] = summary \n",
    "df_full = pd.concat(summaries, join=\"outer\", axis=1)\n",
    "df_full"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_full.to_csv(\"summaries_all_alpha_weight_1_10_compm_RM.csv\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We investigate serine and cysteine"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "alphas = [i/10 for i in range(1,10)]\n",
    "serine_DP = []\n",
    "serine_SA = []\n",
    "cysteine_DP = []\n",
    "cysteine_SA = []\n",
    "for i,row in df_full.iterrows():\n",
    "    for a in alphas:\n",
    "        row_a = row[a]\n",
    "        if row_a[\"Exchanges\"] == \"EX_cys__L_e\":\n",
    "            cysteine_DP.append(row_a[\"DP_83VPs_KB5 Shuttel Flux\"])\n",
    "            cysteine_SA.append(row_a[\"iYS854 Shuttel Flux\"])\n",
    "        if row_a[\"Exchanges\"] == \"EX_ser__D_e\":\n",
    "            serine_DP.append(row_a[\"DP_83VPs_KB5 Shuttel Flux\"])\n",
    "            serine_SA.append(row_a[\"iYS854 Shuttel Flux\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[-9.996433705799296,\n",
       " -9.994040136474734,\n",
       " -9.9910602047121,\n",
       " -9.988080272949468,\n",
       " -9.985100341186834,\n",
       " -9.982120409424201,\n",
       " -9.979140477661568,\n",
       " -9.976160545898935,\n",
       " -9.973180614136302]"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cysteine_DP"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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      ],
      "text/plain": [
       "<Figure size 432x288 with 2 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig, axs = plt.subplots(1,2)\n",
    "axs[0].set_title(\"Cysteine\")\n",
    "axs[0].plot(alphas, cysteine_DP)\n",
    "axs[0].plot(alphas, cysteine_SA)\n",
    "axs[1].set_title(\"Serine D\")\n",
    "axs[1].plot(alphas, serine_DP)\n",
    "axs[1].plot(alphas, serine_SA)\n",
    "axs[1].legend([\"DP\", \"SA\"])\n",
    "fig.savefig(\"Serien_cyteine_plot_RM.pdf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Glucose dependence?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "# For community \n",
    "model.set_weights([1,10])\n",
    "model.slim_optimize()\n",
    "medium = model.medium\n",
    "glc = np.linspace(0,100,100) \n",
    "growth = []\n",
    "for g in glc:\n",
    "    medium[\"EX_glc__D_e\"] = g \n",
    "    model.set_medium(medium)\n",
    "    growth.append(model.slim_optimize())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    </g>\r\n",
       "   </g>\r\n",
       "  </g>\r\n",
       " </g>\r\n",
       " <defs>\r\n",
       "  <clipPath id=\"p34ffab98be\">\r\n",
       "   <rect height=\"217.44\" width=\"334.8\" x=\"40.603125\" y=\"22.318125\"/>\r\n",
       "  </clipPath>\r\n",
       " </defs>\r\n",
       "</svg>\r\n"
      ],
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.plot(glc, growth)\n",
    "plt.xlabel(\"Glucose concentration\")\n",
    "plt.ylabel(\"Growth\")\n",
    "plt.title(\"Glucose community dependences weights DP:10, SA:1\")\n",
    "plt.ylabel(\"Growth\")\n",
    "plt.savefig(\"community_glucose_dependence_weights10_1_RM.png\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1.5457511759833413"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Growth without glucose\n",
    "growth[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "# For community \n",
    "model.set_weights([1,1])\n",
    "model.slim_optimize()\n",
    "medium = model.medium\n",
    "glc = np.linspace(0,100,100) \n",
    "growth = []\n",
    "for g in glc:\n",
    "    medium[\"EX_glc__D_e\"] = g \n",
    "    model.set_medium(medium)\n",
    "    growth.append(model.slim_optimize())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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       "    </g>\r\n",
       "   </g>\r\n",
       "  </g>\r\n",
       " </g>\r\n",
       " <defs>\r\n",
       "  <clipPath id=\"pd6aea771d5\">\r\n",
       "   <rect height=\"217.44\" width=\"334.8\" x=\"43.78125\" y=\"22.318125\"/>\r\n",
       "  </clipPath>\r\n",
       " </defs>\r\n",
       "</svg>\r\n"
      ],
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "plt.plot(glc, growth)\n",
    "plt.xlabel(\"Glucose concentration\")\n",
    "plt.ylabel(\"Growth\")\n",
    "plt.title(\"Glucose community dependences weights DP:1, SA:1\")\n",
    "plt.savefig(\"community_glucose_dependence_weights1_1_RM.png\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1.5457511759833893"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Growth without glucose\n",
    "growth[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Growth:  0.282365392532252\n",
      "Growth:  2.558694612613397\n"
     ]
    }
   ],
   "source": [
    "# For single models\n",
    "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": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 0, 'glc concentration')"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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   ],
   "source": [
    "growths = []\n",
    "x = np.linspace(0,100,100)\n",
    "for c in x:\n",
    "    with model_DP as model:\n",
    "        medium = model.medium \n",
    "        medium[\"EX_glc__D_e\"] = c \n",
    "        model.medium = medium \n",
    "        growths.append(model.slim_optimize())\n",
    "plt.plot(x,growths)\n",
    "plt.xlabel(\"glc concentration\") "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 0, 'glc concentration')"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
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   ],
   "source": [
    "growths = []\n",
    "x = np.linspace(0,100,100)\n",
    "for c in x:\n",
    "    with model_SA as model:\n",
    "        medium = model.medium \n",
    "        medium[\"EX_glc__D_e\"] = c \n",
    "        model.medium = medium \n",
    "        growths.append(model.slim_optimize())\n",
    "plt.plot(x,growths)\n",
    "plt.xlabel(\"glc concentration\")         "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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