Metabolism in Sorghum.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Modelling metabolism in SORGHUM"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generating SORGHUM core model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra import io\n",
    "from cobra.core import Metabolite\n",
    "\n",
    "#import sbml file\n",
    "model = io.sbml.create_cobra_model_from_sbml_file(\"/home/sanu/Documents/Scripts/git/plantcoremetabolism-model/PlantCoreMetabolism_v1_2_3.xml\")\n",
    "\n",
    "#change Biomass_tx to Protein_biomass\n",
    "rxn = model.reactions.get_by_id(\"Biomass_tx\")\n",
    "rxn.id = \"Protein_biomass_tx\"\n",
    "for met in [\"K_b\",\"Ca_b\",\"Mg_b\"]:\n",
    "    met  = model.metabolites.get_by_id(met)\n",
    "    coeff = rxn.metabolites.get(met)\n",
    "    rxn.add_metabolites({met:-1*coeff})\n",
    "met = Metabolite(\"Protein_b\",name=\"Protein_biomass\")\n",
    "met.compartment=\"b\"\n",
    "formula_dict = rxn.check_mass_balance()\n",
    "met.formula = \"\".join([atom+str(formula_dict[atom]*-1) for atom in formula_dict.keys() if atom != \"charge\"])\n",
    "met.charge = formula_dict[\"charge\"]*-1\n",
    "rxn.add_metabolites({met:1})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pythoncyc\n",
    "from Functions import *\n",
    "\n",
    "cyc = pythoncyc.select_organism(\"sorghumbicolor\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--------------\n",
      "This list of metabolic reactions are ignored\n",
      "['RXN_9650_p', '2_KETO_ADIPATE_DEHYDROG_RXN_m', 'Phytol_biosynthesis_p', 'CYSTEINE_AMINOTRANSFERASE_RXN_m', 'GLYCINE_TRNA_LIGASE_RXN_c', 'RXN66_1_c', 'RXN_9648_p', 'RXN-9651', 'Plastidial_ATP_Synthase_p', 'GGPP_biosynthesis_p', 'RXN_9653_p', 'lycopene_biosynthesis_p', 'RXN_2141_p', 'SUCCINYL_COA_HYDROLASE_RXN_m', 'PROTON_ATPase_c', 'MDA_Fd_Ascorbate_p', 'MercaptoPyruvateSulfurtransferase_m', 'Phytol_degradation_p', 'RXN_9652_p', 'A_B_oxidation_x', 'unlProtHYPO_c', 'Mitochondrial_ATP_Synthase_m', 'IPP_biosynthesis_c', 'Mehler_Reaction_p', 'Beta_Oxidation_x', 'HMBPP_synthesis_p', 'OROTATE_REDUCTASE_NADH_RXN_p', 'Ferredoxin_Plastoquinone_Reductase_p', 'RXN_9651_p', 'NADPH_Dehydrogenase_p', 'Plastoquinol_Oxidase_p', 'SUCCINATE_COA_LIGASE_GDP_FORMING_RXN_m', 'RXN_1781_v', 'PREPHENATE_DEHYDROGENASE_NADP_RXN_p', 'PREPHENATEDEHYDROG_RXN_p', 'MALEYLACETOACETATE_ISOMERASE_RXN_c', 'RXN_9654_p', 'LCYSDESULF_RXN_c', 'RXN_9958_NAD_m', 'HEXOKINASE_RXN_MANNOSE_c', 'PYRUVDEH_RXN_p', 'PYRUVDEH_RXN_m', 'RXN_15130_p', '2_AMINOADIPATE_AMINOTRANSFERASE_RXN_c', 'GLURS_RXN_c', 'ALLYSINE_DEHYDROG_RXN_c', 'GLUTARYL_COA_DEHYDROG_RXN_m', 'GLUTACONYL_COA_DECARBOXYLASE_RXN_x']\n",
      "--------------\n",
      "RXN_12486_c\n",
      "3_PERIOD_2_PERIOD_1_PERIOD_48_RXN_v\n",
      "2_PERIOD_7_PERIOD_7_PERIOD_34_RXN_c\n",
      "CELLULOSE_SYNTHASE_GDP_FORMING_RXN_c\n",
      "RXN_10773_c\n",
      "3_PERIOD_2_PERIOD_1_PERIOD_48_RXN_c\n",
      "MALTODEG_RXN_c\n",
      "RXN_1841_v\n"
     ]
    }
   ],
   "source": [
    "model = addGPR2Models(model,cyc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "899"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(model.genes)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Use biomass composition to generate biomass equations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "df = pd.read_csv(\"/home/sanu/biomass_sorghum.csv\")\n",
    "\n",
    "\n",
    "from cobra.core import Reaction\n",
    "\n",
    "rxn = Reaction(\"Biomass_leaf_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    rxn.add_metabolites({model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][\"leaf\"])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "model.add_reaction(rxn)\n",
    "\n",
    "rxn = Reaction(\"Biomass_stem_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    rxn.add_metabolites({model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][\"stem\"])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "model.add_reaction(rxn)\n",
    "\n",
    "rxn = Reaction(\"Biomass_root_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    rxn.add_metabolites({model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][\"root\"])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "model.add_reaction(rxn)\n",
    "\n",
    "rxn = Reaction(\"Biomass_seed_tx\")\n",
    "for met in df[\"Unnamed: 0\"]:\n",
    "    rxn.add_metabolites({model.metabolites.get_by_id(met):-1*float(df[df[\"Unnamed: 0\"]==met][\"seed\"])})\n",
    "rxn.lower_bound = 0\n",
    "rxn.upper_bound = 1000\n",
    "model.add_reaction(rxn)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run stem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Biomass flux =0.684546591491\n"
     ]
    }
   ],
   "source": [
    "from cobra import flux_analysis\n",
    "stem_model = model.copy()\n",
    "stem_model.reactions.GLC_tx.upper_bound = 0\n",
    "stem_model.reactions.GLC_tx.lower_bound = 0\n",
    "stem_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "stem_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "stem_model.reactions.Photon_tx.upper_bound = 0\n",
    "stem_model.reactions.Photon_tx.lower_bound = 0\n",
    "stem_model.reactions.Biomass_stem_tx.objective_coefficient=1\n",
    "flux_analysis.parsimonious.pfba(stem_model)\n",
    "print(\"Biomass flux =\"+str(stem_model.reactions.Biomass_stem_tx.flux))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run root"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Biomass flux =1000.0\n"
     ]
    }
   ],
   "source": [
    "from cobra import flux_analysis\n",
    "root_model = model.copy()\n",
    "root_model.reactions.GLC_tx.upper_bound = 0\n",
    "root_model.reactions.GLC_tx.lower_bound = 0\n",
    "root_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "root_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "root_model.reactions.Photon_tx.upper_bound = 0\n",
    "root_model.reactions.Photon_tx.lower_bound = 0\n",
    "root_model.reactions.Biomass_root_tx.objective_coefficient=1\n",
    "flux_analysis.parsimonious.pfba(root_model)\n",
    "print(\"Biomass flux =\"+str(root_model.reactions.Biomass_root_tx.flux))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run seed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Biomass flux =0.776343545291\n"
     ]
    }
   ],
   "source": [
    "from cobra import flux_analysis\n",
    "seed_model = model.copy()\n",
    "seed_model.reactions.GLC_tx.upper_bound = 0\n",
    "seed_model.reactions.GLC_tx.lower_bound = 0\n",
    "seed_model.reactions.Sucrose_tx.upper_bound = 1\n",
    "seed_model.reactions.Sucrose_tx.lower_bound = 1\n",
    "seed_model.reactions.Photon_tx.upper_bound = 0\n",
    "seed_model.reactions.Photon_tx.lower_bound = 0\n",
    "seed_model.reactions.Biomass_seed_tx.objective_coefficient=1\n",
    "sol=flux_analysis.parsimonious.pfba(seed_model)\n",
    "print(\"Biomass flux =\"+str(seed_model.reactions.Biomass_seed_tx.flux))\n",
    "\n",
    "    \n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generate diel leaf model\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Function to make multiple copies of compartments\n",
    "#args: 1) original cobra model 2) final model 3) number of copies\n",
    "def multiply_compartments(old_model, new_model, x):\n",
    "\tfor y in range(0, x):\n",
    "\t\tfor compartment in old_model.compartments:\n",
    "\t\t\tnew_model.compartments.update({str(compartment + str(y+1)) : old_model.compartments.get(compartment)})\n",
    "\n",
    "#Function to make multiple copies of reactions and metabolites\n",
    "#args: 1) original cobra model 2) final model 3) number of copies\n",
    "def multiply_rxnmet(old_model, new_model, x):\n",
    "\tfrom cobra.core import Reaction,Metabolite, Model\n",
    "\tfor y in range(0, x):\n",
    "\t\tfor reaction in old_model.reactions:\n",
    "\t\t\tnewid = str(reaction.id + str(y+1))\n",
    "\t\t\tnew1 = Reaction(newid)\n",
    "\t\t\tnew1.name = reaction.name\n",
    "\t\t\tnew1.subsystem = reaction.subsystem\n",
    "\t\t\tnew1.lower_bound = reaction.lower_bound\n",
    "\t\t\tnew1.upper_bound = reaction.upper_bound\n",
    "\t\t\tfor metabolite in reaction.metabolites:\n",
    "\t\t\t\tnewidm = str(metabolite.id + str(y+1))\n",
    "\t\t\t\tnewm = Metabolite(newidm)\n",
    "\t\t\t\tnewm.name = metabolite.name\n",
    "\t\t\t\tnewm.formula = metabolite.formula\n",
    "\t\t\t\tnewm.compartment = str(metabolite.compartment + str(y+1))\n",
    "\t\t\t\tnewm.charge = metabolite.charge\n",
    "\t\t\t\tnew1.add_metabolites({newm : reaction.metabolites.get(metabolite)})\n",
    "\t\t\tnew_model.add_reaction(new1)\n",
    "\n",
    "#Function to generate model stats\n",
    "#args: 1) a cobra model\n",
    "def check_model(model):\n",
    "\tprint \"Reactions:\"+str(len(model.reactions))\n",
    "\tprint \"Metabolites:\"+str(len(model.metabolites))\n",
    "\tprint \"Compartments:\"+str(len(model.compartments))+\"\\n\"\n",
    "\n",
    "#Function to add reversible metabolite transfer reactions\n",
    "#args: 1)a text file with metabolite names 2)a cobra model 3)compartment metaboli-\n",
    "#-te is transferred from 4)compartment metabolite is transferred to\n",
    "def allow_transfer(list_doc, model, from_mod, to_mod):\n",
    "\tfrom cobra.core import Reaction,Metabolite, Model\n",
    "\ta = open(list_doc)\n",
    "\tfor line in a:\n",
    "\t\tb = str(line).replace(\" \", \"\").replace(\"\\n\", \"\").replace(\"\\r\", \"\")\n",
    "\t\tnewid = str(\"EX_\" + b + \"_\" + str(from_mod) + \"_\" + str(to_mod))\n",
    "\t\tnew1 = Reaction(newid)\n",
    "\t\tmodel.add_reaction(new1)\n",
    "\t\tnew1.name = str(\"Transfer of\" + b + \"from\" + str(from_mod) + \"to\" + str(to_mod))\n",
    "\t\tnew1.lower_bound = -1000\n",
    "\t\tnew1.upper_bound = 1000\n",
    "\t\tnew1.add_metabolites({str(b + str(from_mod)) : -1, str(b + str(to_mod)) : 1})\n",
    "\n",
    "#Function to add metabolite transfer reactions\n",
    "#args: 1)a text file with metabolite names 2)a cobra model 3)compartment metaboli-\n",
    "#-te is transferred from 4)compartment metabolite is transferred to\n",
    "def allow_transfer_oneway(list_doc, model, from_mod, to_mod):\n",
    "\tfrom cobra.core import Reaction,Metabolite, Model\n",
    "\ta = open(list_doc)\n",
    "\tfor line in a:\n",
    "\t\tb = str(line).replace(\" \", \"\").replace(\"\\n\", \"\").replace(\"\\r\", \"\")\n",
    "\t\tnewid = str(\"EX_\" + b + \"_\" + str(from_mod) + \"_\" + str(to_mod) + \"ow\")\n",
    "\t\tnew1 = Reaction(newid)\n",
    "\t\tmodel.add_reaction(new1)\n",
    "\t\tnew1.name = str(\"Transfer of\" + b + \"from\" + str(from_mod) + \"to\" + str(to_mod) + \"_ow\")\n",
    "\t\tnew1.lower_bound = 0\n",
    "\t\tnew1.upper_bound = 1000\n",
    "\t\tnew1.add_metabolites({str(b + str(from_mod)) : -1, str(b + str(to_mod)) : 1}) \n",
    "\n",
    "\n",
    "\n",
    "\n",
    "#Function to generate C4 leaf model from a model of plant primary metabolism\n",
    "#args 1)core model 2)text file listing metabolites allowed to transfer between M and BS 3)text file list-\n",
    "#-ing amino acid transferred between day and night 4) text file listing non AA metabolite transferred be-\n",
    "#-tween day and night\n",
    "#output 1) a C4 model\n",
    "def generateC4leafmodel(source_model,M_BS_transferlist=\"met2transfer_M_BS_C4.txt\",Day_night_transferlist_AA=\"met2transfer_AA.txt\",Day_night_transferlist_nonAA=\"met2transfer_nonAA.txt\"):\n",
    "\tfrom cobra.core import Model,Metabolite,Reaction\n",
    "\t# Making C4 model\n",
    "\tC4_model = Model(\"C4_diel_model\")\n",
    "\t\n",
    "\t#Mulitplying compartments, reactions, metabolites\n",
    "\tmultiply_compartments(source_model, C4_model, 4)\n",
    "\tmultiply_rxnmet(source_model, C4_model, 4)\n",
    "\t\n",
    "\t#creating compartment for dummy metabolites\n",
    "\tC4_model.compartments.update({\"f\" : \"Fake\"})\n",
    "\t\n",
    "\tbackup_for_C3 = C4_model.copy()\n",
    "\t\n",
    "\t########          SETTING CONSTRAINTS for C4\n",
    "\t#check_model(C4_model)\n",
    "\t\n",
    "\t#Sugar transport\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"Sucrose_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"Sucrose_tx\" + str(i))).lower_bound = 0\n",
    "\t\tC4_model.reactions.get_by_id(str(\"GLC_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"GLC_tx\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#Diel constraints\n",
    "\tfor i in (2, 4):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"Photon_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"Photon_tx\" + str(i))).lower_bound = 0 \n",
    "\tC4_model.reactions.get_by_id(str(\"Photon_tx1\")).upper_bound = C4_model.reactions.get_by_id(str(\"Photon_tx1\")).lower_bound = 600\n",
    "\tC4_model.reactions.get_by_id(str(\"Photon_tx3\")).upper_bound = C4_model.reactions.get_by_id(str(\"Photon_tx3\")).lower_bound = 400\n",
    "\t\n",
    "\t#CO2 constraints\n",
    "\tC4_model.reactions.get_by_id(\"CO2_tx3\").upper_bound = C4_model.reactions.get_by_id(\"CO2_tx3\").lower_bound = 0 \n",
    "\tC4_model.reactions.get_by_id(\"CO2_tx4\").upper_bound = C4_model.reactions.get_by_id(\"CO2_tx4\").lower_bound = 0 \n",
    "\t\n",
    "\tC4_model.reactions.get_by_id(\"CO2_tx1\").lower_bound = 0\n",
    "\tC4_model.reactions.get_by_id(\"CO2_tx2\").upper_bound = 0\n",
    "\t\n",
    "\t#NH4 import\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"NH4_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"NH4_tx\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#Nitrate ratio day:night\n",
    "\tmet = Metabolite(\"Nitrate_pseudo\")\n",
    "\tmet.name = \"Nitrate_pseudo\"\n",
    "\tmet.compartment = \"f\"\n",
    "\tmet.charge = 0\n",
    "\tfor i in (1,3):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"Nitrate_tx\" + str(i))).add_metabolites({met : 2})\n",
    "\tfor i in (2,4):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"Nitrate_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\t\n",
    "\t#Rubisco oxygenase\n",
    "\tfor i in range(1,5):\n",
    "\t\tmet = Metabolite(\"Rubisco_pseudo\" + str(i))\n",
    "\t\tmet.name = \"Rubisco_pseudo\" + str(i)\n",
    "\t\tmet.compartment = \"f\"\n",
    "\t\tmet.charge = 0\n",
    "\t\tC4_model.reactions.get_by_id(str(\"RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p\" + str(i))).add_metabolites({met : 1})\n",
    "\t\tC4_model.reactions.get_by_id(str(\"RXN_961_p\" + str(i))).add_metabolites({met : -20})\n",
    "\t\n",
    "\t#Rubsico localisation\n",
    "\tfor i in (1,2):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"RIBULOSE_BISPHOSPHATE_CARBOXYLASE_RXN_p\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#GDH localisation\n",
    "\tfor i in (1,2):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"GLYOHMETRANS_RXN_m\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"GLYOHMETRANS_RXN_m\" + str(i))).lower_bound = 0\n",
    "\t\tC4_model.reactions.get_by_id(str(\"GCVMULTI_RXN_m\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"GCVMULTI_RXN_m\" + str(i))).lower_bound =  0\n",
    "\t\n",
    "\t#Maintainence costs\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).lower_bound = 19.5\n",
    "\t\tmet = Metabolite(str(\"Maint_pseudo\" + str(i)))\n",
    "\t\tmet.name = str(\"Maint_pseudo\" + str(i))\n",
    "\t\tmet.compartment = \"f\"\n",
    "\t\tmet.charge = 0\n",
    "\t\tC4_model.reactions.get_by_id(str(\"ATPase_tx\" + str(i))).add_metabolites({met : 1})\n",
    "\t\tC4_model.reactions.get_by_id(str(\"NADPHoxc_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\t\tC4_model.reactions.get_by_id(str(\"NADPHoxm_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\t\tC4_model.reactions.get_by_id(str(\"NADPHoxp_tx\" + str(i))).add_metabolites({met : -3})\n",
    "\t\n",
    "\t#plastid enolase constraint\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"2PGADEHYDRAT_RXN_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"2PGADEHYDRAT_RXN_p\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#plastoquinol oxidase constraint\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"Plastoquinol_Oxidase_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"Plastoquinol_Oxidase_p\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#Mesophyll starch synthase constraint\n",
    "\tfor i in range(1,3):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"GLYCOGENSYN_RXN_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"GLYCOGENSYN_RXN_p\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#plastid hexose transport constraint\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(str(\"G6P_Pi_pc\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"G6P_Pi_pc\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#switching off PSII\n",
    "\t#for i in (3, 4):\n",
    "\t#\tC4_model.reactions.get_by_id(str(\"PSII_RXN_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"PSII_RXN_p\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#\"biomass\"constraint\n",
    "\t#for i in range(1,5):\n",
    "\t#\tC4_model.reactions.get_by_id(str(\"Biomass_tx\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"Biomass_tx\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#choice of decarboxylating enzyme\n",
    "\t#for i in (3,4):\n",
    "\t\t#C4_model.reactions.get_by_id(str(\"MALIC_NAD_RXN_m\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"MALIC_NAD_RXN_m\" + str(i))).lower_bound = 0\n",
    "\t\t#C4_model.reactions.get_by_id(str(\"MALIC_NADP_RXN_p\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"MALIC_NADP_RXN_p\" + str(i))).lower_bound = 0\n",
    "\t\t#C4_model.reactions.get_by_id(str(\"MALIC_NADP_RXN_c\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"MALIC_NADP_RXN_c\" + str(i))).lower_bound = 0\n",
    "\t\t#C4_model.reactions.get_by_id(str(\"PEPCARBOXYKIN_RXN_c\" + str(i))).upper_bound = C4_model.reactions.get_by_id(str(\"PEPCARBOXYKIN_RXN_c\" + str(i))).lower_bound = 0\n",
    "\t\n",
    "\t#metabolite exchanges\n",
    "\tallow_transfer(M_BS_transferlist, C4_model, 1, 3)\n",
    "\tallow_transfer(M_BS_transferlist, C4_model, 2, 4)\n",
    "\tallow_transfer_oneway(Day_night_transferlist_AA, C4_model, 1, 2)\n",
    "\tallow_transfer_oneway(Day_night_transferlist_AA, C4_model, 3, 4)\n",
    "\tallow_transfer(Day_night_transferlist_nonAA, C4_model, 1, 2)\n",
    "\tallow_transfer(Day_night_transferlist_nonAA, C4_model, 3, 4)\n",
    "\t\n",
    "\t# Carbohydrate transfer constraint\n",
    "\tC4_model.reactions.get_by_id(\"EX_SUCROSE_c_1_3\").upper_bound = C4_model.reactions.get_by_id(\"EX_SUCROSE_c_1_3\").lower_bound = 0\n",
    "\tC4_model.reactions.get_by_id(\"EX_SUCROSE_c_2_4\").upper_bound = C4_model.reactions.get_by_id(\"EX_SUCROSE_c_2_4\").lower_bound = 0\n",
    "\tC4_model.reactions.get_by_id(\"EX_MALTOSE_p_1_3\").upper_bound = C4_model.reactions.get_by_id(\"EX_MALTOSE_p_1_3\").lower_bound = 0\n",
    "\tC4_model.reactions.get_by_id(\"EX_MALTOSE_p_2_4\").upper_bound = C4_model.reactions.get_by_id(\"EX_MALTOSE_p_2_4\").lower_bound = 0\n",
    "\t\n",
    "\t# Setting NAD-GAPDH to only run in the direction of glycolysis \n",
    "\tfor i in range(1, 5):\n",
    "\t\tC4_model.reactions.get_by_id(\"GAPOXNPHOSPHN_RXN_c\"+str(i)).upper_bound = 4000\n",
    "\t\tC4_model.reactions.get_by_id(\"GAPOXNPHOSPHN_RXN_c\"+str(i)).lower_bound = 0\n",
    "\t\tC4_model.reactions.get_by_id(\"GAPOXNPHOSPHN_RXN_p\"+str(i)).upper_bound = 4000\n",
    "\t\tC4_model.reactions.get_by_id(\"GAPOXNPHOSPHN_RXN_p\"+str(i)).lower_bound = 0\n",
    "\t\n",
    "\t#CREATE PHLOEM METABOLIE\n",
    "\tfor i in range(3,5):\n",
    "\t\tmet = Metabolite(\"X_Phloem_contribution_t\"+str(i))\n",
    "\t\tC4_model.reactions.get_by_id(\"Phloem_output_tx\"+str(i)).add_metabolites({met:1})\n",
    "\t\n",
    "\t#setting the total output with 3:1 ratio\n",
    "\treac = Reaction(\"Total_Output_tx\")\n",
    "\treac.name = \"Total_Output_tx\"\n",
    "\tC4_model.add_reaction(reac)\n",
    "\tC4_model.reactions.get_by_id(\"Total_Output_tx\").add_metabolites({\"X_Phloem_contribution_t3\" : -0.75, \"X_Phloem_contribution_t4\" : -0.25})\n",
    "\t#print(C4_model.reactions.get_by_id(\"Total_Output_tx\"))\n",
    "\t#check_model(C4_model)\n",
    "\t\n",
    "\t# Increasing model upper bounds\n",
    "\tfor rxn in C4_model.reactions:\n",
    "\t\tif rxn.upper_bound == 1000:\n",
    "\t\t\trxn.upper_bound = 4000\n",
    "\t\tif rxn.lower_bound == -1000:\n",
    "\t\t\trxn.lower_bound = -4000\n",
    "\t\n",
    "\t# Introducing a continuous apoplast\n",
    "\tfor i in range(1, 5):\n",
    "\t\trxn = Reaction(\"H_mc\"+str(i))\n",
    "\t\trxn.id = \"H_mc3\"+str(i)\n",
    "\t\trxn.upper_bound = 4000\n",
    "\t\trxn.lower_bound = -4000\n",
    "\t\tC4_model.add_reaction(rxn)\n",
    "\t\trxn.add_metabolites({\"PROTON_c\"+str(i) : -1, \"PROTON_m\"+str(i) : 1})\n",
    "\t\n",
    "\tfor i in range(1,5):\n",
    "\t\tC4_model.reactions.get_by_id(\"unlProtHYPO_c\"+str(i)).upper_bound = C4_model.reactions.get_by_id(\"unlProtHYPO_c\"+str(i)).lower_bound = 0\n",
    "\t\trxn = Reaction(\"H_ec\"+str(i))\n",
    "\t\trxn.name = \"H_ec\"+str(i)\n",
    "\t\trxn.upper_bound = 4000\n",
    "\t\trxn.lower_bound = 0\n",
    "\t\tC4_model.add_reaction(rxn)\n",
    "\t\trxn.add_metabolites({\"PROTON_c\"+str(i) : 1, \"PROTON_e\"+str(i) : -1})\n",
    "\t\tif i == 1:\n",
    "\t\t\tfor met in C4_model.metabolites.query(\"_e\"+str(i)):\n",
    "\t\t\t\tif not met.id == \"Photon_e\"+str(i):\n",
    "\t\t\t\t\tnewmet = Metabolite(str(met.id)+\"3\")\n",
    "\t\t\t\t\tnewmet.name = str(met.id)+\"3\"\n",
    "\t\t\t\t\tnewmet.compartment = str(met.compartment)+\"3\"\n",
    "\t\t\t\t\tnewmet.formula = met.formula\n",
    "\t\t\t\t\tnewmet.charge = met.charge\n",
    "\t\t\t\t\tfor rxn in met.reactions:\n",
    "\t\t\t\t\t\tj = rxn.metabolites.get(met)\n",
    "\t\t\t\t\t\trxn.add_metabolites({met : -j, newmet : j})\n",
    "\t\t\t\t\t\tif str(rxn.id).endswith(\"_tx\"+str(i)):\n",
    "\t\t\t\t\t\t\tif not rxn.id == \"Phloem_output_tx1\":\n",
    "\t\t\t\t\t\t\t\tif not rxn.id == \"CO2_tx1\":\n",
    "\t\t\t\t\t\t\t\t\tnewid = str(rxn.id + \"3\")\n",
    "\t\t\t\t\t\t\t\t\trxn.id = newid\n",
    "\t\tif i == 3:\n",
    "\t\t\tfor met in C4_model.metabolites.query(\"_e\"+str(i)):\n",
    "\t\t\t\tif not met.id == \"Photon_e\"+str(i):\n",
    "\t\t\t\t\tfor newmet in C4_model.metabolites.query(\"_e13\"):\n",
    "\t\t\t\t\t\tmetstart = str(met.id).split(\"_\")[0]\n",
    "\t\t\t\t\t\tif str(newmet.id).startswith(metstart):\n",
    "\t\t\t\t\t\t\tfor rxn in met.reactions:\n",
    "\t\t\t\t\t\t\t\tj = rxn.metabolites.get(met)\n",
    "\t\t\t\t\t\t\t\trxn.add_metabolites({met : -j, newmet : j})\n",
    "\t\t\t\t\t\t\t\tif str(rxn.id).endswith(\"_tx\"+str(i)):\n",
    "\t\t\t\t\t\t\t\t\tif not rxn.id == \"Phloem_output_tx3\":\n",
    "\t\t\t\t\t\t\t\t\t\tif not rxn.id == \"CO2_tx3\":\n",
    "\t\t\t\t\t\t\t\t\t\t\trxn.upper_bound = rxn.lower_bound = 0\n",
    "\t\tif i == 2:                    \n",
    "\t\t\tfor met in C4_model.metabolites.query(\"_e\"+str(i)):\n",
    "\t\t\t\tif not met.id == \"Photon_e\"+str(i):\n",
    "\t\t\t\t\tnewmet = Metabolite(str(met.id)+\"4\")\n",
    "\t\t\t\t\tnewmet.name = str(met.id)+\"4\"\n",
    "\t\t\t\t\tnewmet.compartment = str(met.compartment)+\"4\"\n",
    "\t\t\t\t\tnewmet.formula = met.formula\n",
    "\t\t\t\t\tnewmet.charge = met.charge\n",
    "\t\t\t\t\tfor rxn in met.reactions:\n",
    "\t\t\t\t\t\tj = rxn.metabolites.get(met)\n",
    "\t\t\t\t\t\trxn.add_metabolites({met : -j, newmet : j})\n",
    "\t\t\t\t\t\tif str(rxn.id).endswith(\"_tx\"+str(i)):\n",
    "\t\t\t\t\t\t\tif not rxn.id == \"Phloem_output_tx2\":\n",
    "\t\t\t\t\t\t\t\tif not rxn.id == \"CO2_tx2\":\n",
    "\t\t\t\t\t\t\t\t\tnewid = str(rxn.id + \"4\")\n",
    "\t\t\t\t\t\t\t\t\trxn.id = newid\n",
    "\t\tif i == 4:\n",
    "\t\t\tfor met in C4_model.metabolites.query(\"_e\"+str(i)):\n",
    "\t\t\t\tif not met.id == \"Photon_e\"+str(i):\n",
    "\t\t\t\t\tfor newmet in C4_model.metabolites.query(\"_e24\"):\n",
    "\t\t\t\t\t\tmetstart = str(met.id).split(\"_\")[0]\n",
    "\t\t\t\t\t\tif str(newmet.id).startswith(metstart):\n",
    "\t\t\t\t\t\t\tfor rxn in met.reactions:\n",
    "\t\t\t\t\t\t\t\tj = rxn.metabolites.get(met)\n",
    "\t\t\t\t\t\t\t\trxn.add_metabolites({met : -j, newmet : j})\n",
    "\t\t\t\t\t\t\t\tif str(rxn.id).endswith(\"_tx\"+str(i)):\n",
    "\t\t\t\t\t\t\t\t\tif not rxn.id == \"Phloem_output_tx4\":\n",
    "\t\t\t\t\t\t\t\t\t\tif not rxn.id == \"CO2_tx4\":\n",
    "\t\t\t\t\t\t\t\t\t\t\trxn.upper_bound = rxn.lower_bound = 0\n",
    "\t\n",
    "\t#Restoring the previous constraints for CO2\n",
    "\tC4_model.reactions.get_by_id(\"CO2_ec3\").upper_bound = C4_model.reactions.get_by_id(\"CO2_ec3\").lower_bound = 0 \n",
    "\tC4_model.reactions.get_by_id(\"CO2_ec4\").upper_bound = C4_model.reactions.get_by_id(\"CO2_ec4\").lower_bound = 0 \n",
    "\t\n",
    "\tC4_model.reactions.get_by_id(\"CO2_ec1\").lower_bound = 0\n",
    "\tC4_model.reactions.get_by_id(\"CO2_ec2\").upper_bound = 0\n",
    "\t\n",
    "\t# Optimising...\n",
    "\tC4_model.objective = C4_model.reactions.get_by_id(\"Total_Output_tx\")\n",
    "\tC4_model.reactions.get_by_id(\"Total_Output_tx\").objective_value = 1\n",
    "\treturn C4_model\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Phloem output = \n",
      "6.07213509339\n"
     ]
    }
   ],
   "source": [
    "leaf_model = model.copy()\n",
    "\n",
    "leaf_model = generateC4leafmodel(leaf_model,M_BS_transferlist=\"met2transfer_M_BS_C4.txt\",Day_night_transferlist_AA=\"met2transfer_AA.txt\",Day_night_transferlist_nonAA=\"met2transfer_nonAA.txt\")\n",
    "\n",
    "leaf_model.reactions.Total_Output_tx.objective_coefficient=1\n",
    "flux_analysis.parsimonious.pfba(leaf_model)\n",
    "print(\"Phloem output = \")\n",
    "print(leaf_model.reactions.Total_Output_tx.flux)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Biomass accumulation = \n",
      "0.0312189091084\n"
     ]
    }
   ],
   "source": [
    "leaf_model_sink = model.copy()\n",
    "\n",
    "leaf_model_sink = generateC4leafmodel(leaf_model_sink,M_BS_transferlist=\"met2transfer_M_BS_C4.txt\",Day_night_transferlist_AA=\"met2transfer_AA.txt\",Day_night_transferlist_nonAA=\"met2transfer_nonAA.txt\")\n",
    "\n",
    "met = Metabolite(\"X_Biomass_contribution_day\")\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx1.add_metabolites({met:1})\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx3.add_metabolites({met:1})\n",
    "leaf_model_sink.metabolites.X_Phloem_contribution_t3.remove_from_model()\n",
    "leaf_model_sink.reactions.Total_Output_tx.add_metabolites({met:-3})\n",
    "\n",
    "met = Metabolite(\"X_Biomass_contribution_night\")\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx2.add_metabolites({met:1})\n",
    "leaf_model_sink.reactions.Biomass_leaf_tx4.add_metabolites({met:1})\n",
    "leaf_model_sink.metabolites.X_Phloem_contribution_t4.remove_from_model()\n",
    "leaf_model_sink.reactions.Total_Output_tx.add_metabolites({met:-1})\n",
    "\n",
    "leaf_model_sink.reactions.Total_Output_tx.objective_coefficient=1\n",
    "flux_analysis.parsimonious.pfba(leaf_model_sink)\n",
    "print(\"Biomass accumulation = \")\n",
    "print(leaf_model_sink.reactions.Total_Output_tx.flux)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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