// Created by libAntimony v2.8.0
function carboxylation(kc, S2, K, R, KI, E, S1)
  (((kc*S2)/(S2 + K*(1 + R/KI))*E + (kc*S2)/(S2 + K*(1 + R/KI))*S1) - abs((kc*S2)/(S2 + K*(1 + R/KI))*E - (kc*S2)/(S2 + K*(1 + R/KI))*S1))/2;
end

function PGA_consumption(S1, Rp, Nt, kc, E, R)
  S1/Rp*(R/Nt)*kc*E;
end

function NADPH_production(j, S1, Nt)
  j/2*(S1/Nt);
end

function oxygenation(phi, kc, S2, K, R, KI, E, S1)
  (phi*(((kc*S2)/(S2 + K*(1 + R/KI))*E + (kc*S2)/(S2 + K*(1 + R/KI))*S1) - abs((kc*S2)/(S2 + K*(1 + R/KI))*E - (kc*S2)/(S2 + K*(1 + R/KI))*S1)))/2;
end


model *Model_1()

  // Compartments and Species:
  compartment chloroplast;
  species $RuBP in chloroplast, PGA in chloroplast, NADPH in chloroplast;
  species $CO2 in chloroplast, $O2 in chloroplast, $NADP in chloroplast;

  // Assignment Rules:
  NADP := Nt - NADPH;
  jp := 1/2*(1 - f)*I;
  j := (abs(jp + 467) - abs(jp - 467))/2/65;
  phi := (0.21*(O2/Ko))/(CO2/Kc);

  // Reactions:
  PGA_prod_Vc: $RuBP + $CO2 + 2NADPH => 2PGA; chloroplast*carboxylation(kc, CO2, Kc, O2, Ko, E, RuBP);
  PGA_prod_Vo: $RuBP + $CO2 + 2NADPH => 1.5PGA; chloroplast*oxygenation(phi, kc, CO2, Kc, O2, Ko, E, RuBP);
  PGA_cons: PGA => $RuBP; chloroplast*PGA_consumption(PGA, Rp, Nt, kc, E, NADPH);
  NADPH_prod: $NADP => NADPH; chloroplast*NADPH_production(j, NADP, Nt);

  // Species initializations:
  RuBP = 2;
  PGA = 2.4;
  NADPH = 0.21;
  CO2 = 230;
  O2 = 210;

  // Compartment initializations:
  chloroplast = 1;

  // Variable initializations:
  Nt = 0.5;
  E = 1.33846153846154;
  Rp = 3.2;
  f = 0.23;
  I = 1000;
  Ko = 330;
  Kc = 460;
  kc = 2.5;

  // Other declarations:
  var jp, j, phi;
  const chloroplast, Nt, E, Rp, f, I, Ko, Kc, kc;

  // Unit definitions:
  unit substance = 1e-3 mole;

  // Display Names:
  PGA_prod_Vc is "PGA production - v_c";
  PGA_prod_Vo is "PGA production - v_o";
  PGA_cons is "PGA consumption";
  NADPH_prod is "NADPH production";
end