// This model generated automatically from SBML

// unit definitions
import nsrunit;
unit conversion off;

// SBML property definitions
property sbmlRole=string;
property sbmlName=string;
property sbmlCompartment=string;

// SBML reactions
// E1: RuBP_ch x_CO2 <=> 2PGA_ch 
// E2: PGA_ch ATP_ch <=> BPGA_ch ADP_ch 
// E3: x_NADPH_ch BPGA_ch x_Proton_ch <=> x_NADP_ch GAP_ch Pi_ch 
// E4: GAP_ch => DHAP_ch 
// E5: GAP_ch DHAP_ch => FBP_ch 
// E6: FBP_ch <=> F6P_ch Pi_ch 
// E7: GAP_ch F6P_ch => X5P_ch E4P_ch 
// E8: DHAP_ch E4P_ch => SBP_ch 
// E9: SBP_ch <=> Pi_ch S7P_ch 
// E10: S7P_ch GAP_ch => R5P_ch X5P_ch 
// E11: R5P_ch => Ru5P_ch 
// E12: X5P_ch => Ru5P_ch 
// E13: Ru5P_ch ATP_ch <=> RuBP_ch ADP_ch 
// E14: F6P_ch => G6P_ch 
// E15: G6P_ch => G1P_ch 
// light_reaction: Pi_ch ADP_ch <=> ATP_ch 
// E16: ATP_ch G1P_ch <=> x_Starch_ch ADP_ch 2Pi_ch 
// E17: x_Starch_ch Pi_ch <=> G1P_ch 
// E18_DHAP: x_Pi_cyt DHAP_ch <=> x_DHAP_cyt Pi_ch 
// E18_PGA: x_Pi_cyt PGA_ch <=> x_PGA_cyt Pi_ch 
// E18_GAP: x_Pi_cyt GAP_ch <=> x_GAP_cyt Pi_ch 

math main {
  realDomain time second;
  time.min=0;
  extern time.max;
  extern time.delta;

  // variable definitions
  real chloroplast = 1 L;
  real cytosol = 1 L;
  real Light_on = 1;
  real x_CO2 = 1 mM;
  real RuBP_ch(time) mM;
  real PGA_ch(time) mM;
  real ATP_ch(time) mM;
  real BPGA_ch(time) mM;
  real x_NADPH_ch = .21 mM;
  real GAP_ch(time) mM;
  real Pi_ch(time) mM;
  real DHAP_ch(time) mM;
  real FBP_ch(time) mM;
  real F6P_ch(time) mM;
  real E4P_ch(time) mM;
  real X5P_ch(time) mM;
  real SBP_ch(time) mM;
  real S7P_ch(time) mM;
  real R5P_ch(time) mM;
  real Ru5P_ch(time) mM;
  real x_Pi_cyt = .5 mM;
  real x_GAP_cyt = 1 mM;
  real G6P_ch(time) mM;
  real x_NADP_ch = .29 mM;
  real x_PGA_cyt = 1 mM;
  real ADP_ch(time) mM;
  real x_DHAP_cyt = 1 mM;
  real x_Proton_ch = 2.512E-5 mM;
  real G1P_ch(time) mM;
  real x_Starch_ch = 1 mM;
  real E1(time) millikatal;
  real Rbco_vm = 340;
  real Rbco_km = .02;
  real Rbco_KiPGA = .84;
  real Rbco_KiFBP = .04;
  real Rbco_KiSBP = .075;
  real Rbco_KiPi = .9;
  real Rbco_KiNADPH = .07;
  real E2(time) millikatal;
  real PGK_v = 5E8;
  real q2 = 3.1E-4;
  real E3(time) millikatal;
  real G3Pdh_v = 5E8;
  real q3 = 1.6E7;
  real E4(time) millikatal;
  real TPI_v = 5E8;
  real q4 = 22;
  real E5(time) millikatal;
  real F_Aldo_v = 5E8;
  real q5 = 7.1;
  real E6(time) millikatal;
  real FBPase_ch_vm = 200;
  real FBPase_ch_km = .03;
  real FBPase_ch_KiF6P = .7;
  real FBPase_ch_KiPi = 12;
  real E7(time) millikatal;
  real F_TKL_v = 5E8;
  real q7 = .084;
  real E8(time) millikatal;
  real E_Aldo_v = 5E8;
  real q8 = 13;
  real E9(time) millikatal;
  real SBPase_ch_vm = 40;
  real SBPase_ch_km = .013;
  real SBPase_ch_KiPi = 12;
  real E10(time) millikatal;
  real G_TKL_v = 5E8;
  real q10 = .85;
  real E11(time) millikatal;
  real R5Piso_v = 5E8;
  real q11 = .4;
  real E12(time) millikatal;
  real X5Pepi_v = 5E8;
  real q12 = .67;
  real E13(time) millikatal;
  real Ru5Pk_ch_vm = 1E4;
  real Ru5Pk_ch_km1 = .05;
  real Ru5Pk_ch_KiPGA = 2;
  real Ru5Pk_ch_KiRuBP = .7;
  real Ru5Pk_ch_KiPi = 4;
  real Ru5Pk_ch_KiADP1 = 2.5;
  real Ru5Pk_ch_km2 = .05;
  real Ru5Pk_ch_KiADP2 = .4;
  real E14(time) millikatal;
  real PGI_v = 5E8;
  real q14 = 2.3;
  real E15(time) millikatal;
  real PGM_v = 5E8;
  real q15 = .058;
  real light_reaction(time) millikatal;
  real LR_vm = 3500;
  real LR_kmADP = .014;
  real LR_kmPi = .3;
  real E16(time) millikatal;
  real StSyn_vm = 40;
  real stsyn_ch_km1 = .08;
  real stsyn_ch_Ki = 10;
  real stsyn_ch_km2 = .08;
  real stsyn_ch_ka1 = .1;
  real stsyn_ch_ka2 = .02;
  real stsyn_ch_ka3 = .02;
  real E17(time) millikatal;
  real StPase_Vm = 40;
  real StPase_km = .1;
  real StPase_kiG1P = .05;
  real E18_DHAP(time) millikatal;
  real TP_Piap_vm = 250;
  real TP_Piap_kDHAP_ch = .077;
  real TP_Piap_kPi_cyt = .74;
  real TP_Piap_kPi_ch = .63;
  real TP_Piap_kPGA_ch = .25;
  real TP_Piap_kGAP_ch = .075;
  real E18_PGA(time) millikatal;
  real PGA_xpMult = .75;
  real E18_GAP(time) millikatal;

  // equations
  when (time=time.min) RuBP_ch = .33644;
  RuBP_ch:time = (-1*E1 + E13)/chloroplast;
  when (time=time.min) PGA_ch = 3.35479;
  PGA_ch:time = (2*E1 + -1*E2 + -1*E18_PGA)/chloroplast;
  when (time=time.min) ATP_ch = .49806;
  ATP_ch:time = (-1*E2 + -1*E13 + light_reaction + -1*E16)/chloroplast;
  when (time=time.min) BPGA_ch = .14825;
  BPGA_ch:time = (E2 + -1*E3)/chloroplast;
  when (time=time.min) GAP_ch = .01334;
  GAP_ch:time = (E3 + -1*E4 + -1*E5 + -1*E7 + -1*E10 + -1*E18_GAP)/chloroplast;
  when (time=time.min) Pi_ch = 1.5662;
  Pi_ch:time = (E3 + E6 + E9 + -1*light_reaction + 2*E16 + -1*E17 + E18_DHAP + E18_PGA + E18_GAP)/chloroplast;
  when (time=time.min) DHAP_ch = .29345;
  DHAP_ch:time = (E4 + -1*E5 + -1*E8 + -1*E18_DHAP)/chloroplast;
  when (time=time.min) FBP_ch = .02776;
  FBP_ch:time = (E5 + -1*E6)/chloroplast;
  when (time=time.min) F6P_ch = 1.36481;
  F6P_ch:time = (E6 + -1*E7 + -1*E14)/chloroplast;
  when (time=time.min) E4P_ch = .41021;
  E4P_ch:time = (E7 + -1*E8)/chloroplast;
  when (time=time.min) X5P_ch = .00363;
  X5P_ch:time = (E7 + E10 + -1*E12)/chloroplast;
  when (time=time.min) SBP_ch = 1.56486;
  SBP_ch:time = (E8 + -1*E9)/chloroplast;
  when (time=time.min) S7P_ch = .00541;
  S7P_ch:time = (E9 + -1*E10)/chloroplast;
  when (time=time.min) R5P_ch = .00599;
  R5P_ch:time = (E10 + -1*E11)/chloroplast;
  when (time=time.min) Ru5P_ch = .00235;
  Ru5P_ch:time = (E11 + E12 + -1*E13)/chloroplast;
  when (time=time.min) G6P_ch = 3.1396;
  G6P_ch:time = (E14 + -1*E15)/chloroplast;
  when (time=time.min) ADP_ch = .00149;
  ADP_ch:time = (E2 + E13 + -1*light_reaction + E16)/chloroplast;
  when (time=time.min) G1P_ch = .18206;
  G1P_ch:time = (E15 + -1*E16 + E17)/chloroplast;
  E1 = Light_on*Rbco_vm*RuBP_ch*chloroplast/(RuBP_ch+Rbco_km*(1+PGA_ch/Rbco_KiPGA+FBP_ch/Rbco_KiFBP+SBP_ch/Rbco_KiSBP+Pi_ch/Rbco_KiPi+x_NADPH_ch/Rbco_KiNADPH));
  E2 = Light_on*PGK_v*chloroplast*(PGA_ch*ATP_ch-BPGA_ch*ADP_ch/q2);
  E3 = Light_on*G3Pdh_v*chloroplast*(BPGA_ch*x_NADPH_ch*x_Proton_ch-x_NADP_ch*GAP_ch*Pi_ch/q3);
  E4 = chloroplast*TPI_v*(GAP_ch-DHAP_ch/q4);
  E5 = F_Aldo_v*chloroplast*(DHAP_ch*GAP_ch-FBP_ch/q5);
  E6 = Light_on*FBPase_ch_vm*FBP_ch*chloroplast/(FBP_ch+FBPase_ch_km*(1+F6P_ch/FBPase_ch_KiF6P+Pi_ch/FBPase_ch_KiPi));
  E7 = chloroplast*F_TKL_v*(F6P_ch*GAP_ch-E4P_ch*X5P_ch/q7);
  E8 = chloroplast*E_Aldo_v*(E4P_ch*DHAP_ch-SBP_ch/q8);
  E9 = Light_on*SBPase_ch_vm*SBP_ch*chloroplast/(SBP_ch+SBPase_ch_km*(1+Pi_ch/SBPase_ch_KiPi));
  E10 = chloroplast*G_TKL_v*(GAP_ch*S7P_ch-X5P_ch*R5P_ch/q10);
  E11 = R5Piso_v*chloroplast*(R5P_ch-Ru5P_ch/q11);
  E12 = chloroplast*X5Pepi_v*(X5P_ch-Ru5P_ch/q12);
  E13 = Light_on*Ru5Pk_ch_vm*Ru5P_ch*chloroplast*ATP_ch/((Ru5P_ch+Ru5Pk_ch_km1*(1+PGA_ch/Ru5Pk_ch_KiPGA+RuBP_ch/Ru5Pk_ch_KiRuBP+Pi_ch/Ru5Pk_ch_KiPi))*(ATP_ch*(1+ADP_ch/Ru5Pk_ch_KiADP1)+Ru5Pk_ch_km2*(1+ADP_ch/Ru5Pk_ch_KiADP2)));
  E14 = PGI_v*chloroplast*(F6P_ch-G6P_ch/q14);
  E15 = PGM_v*chloroplast*(G6P_ch-G1P_ch/q15);
  light_reaction = Light_on*LR_vm*ADP_ch*Pi_ch*chloroplast/((ADP_ch+LR_kmADP)*(Pi_ch+LR_kmPi));
  E16 = StSyn_vm*G1P_ch*ATP_ch*chloroplast/((G1P_ch+stsyn_ch_km1)*(1+ADP_ch/stsyn_ch_Ki)*(ATP_ch+stsyn_ch_km2)+stsyn_ch_km2*Pi_ch/(stsyn_ch_ka1*PGA_ch)+stsyn_ch_ka2*F6P_ch+stsyn_ch_ka3*FBP_ch);
  E17 = StPase_Vm*Pi_ch*chloroplast/(Pi_ch+StPase_km*(1+G1P_ch/StPase_kiG1P));
  E18_DHAP = TP_Piap_vm*DHAP_ch*chloroplast/(TP_Piap_kDHAP_ch*(1+(1+TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/TP_Piap_kPi_ch+PGA_ch/TP_Piap_kPGA_ch+DHAP_ch/TP_Piap_kDHAP_ch+GAP_ch/TP_Piap_kGAP_ch)));
  E18_PGA = PGA_xpMult*TP_Piap_vm*PGA_ch*chloroplast/(TP_Piap_kPGA_ch*(1+(1+TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/TP_Piap_kPi_ch+PGA_ch/TP_Piap_kPGA_ch+DHAP_ch/TP_Piap_kDHAP_ch+GAP_ch/TP_Piap_kGAP_ch)));
  E18_GAP = TP_Piap_vm*GAP_ch*chloroplast/(TP_Piap_kGAP_ch*(1+(1+TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/TP_Piap_kPi_ch+PGA_ch/TP_Piap_kPGA_ch+DHAP_ch/TP_Piap_kDHAP_ch+GAP_ch/TP_Piap_kGAP_ch)));

  // variable properties
  chloroplast.sbmlRole="compartment";
  cytosol.sbmlRole="compartment";
  Light_on.sbmlRole="parameter";
  x_CO2.sbmlRole="species";
  x_CO2.sbmlCompartment="chloroplast";
  RuBP_ch.sbmlRole="species";
  RuBP_ch.sbmlCompartment="chloroplast";
  PGA_ch.sbmlRole="species";
  PGA_ch.sbmlCompartment="chloroplast";
  ATP_ch.sbmlRole="species";
  ATP_ch.sbmlCompartment="chloroplast";
  BPGA_ch.sbmlRole="species";
  BPGA_ch.sbmlCompartment="chloroplast";
  x_NADPH_ch.sbmlRole="species";
  x_NADPH_ch.sbmlCompartment="chloroplast";
  GAP_ch.sbmlRole="species";
  GAP_ch.sbmlCompartment="chloroplast";
  Pi_ch.sbmlRole="species";
  Pi_ch.sbmlCompartment="chloroplast";
  DHAP_ch.sbmlRole="species";
  DHAP_ch.sbmlCompartment="chloroplast";
  FBP_ch.sbmlRole="species";
  FBP_ch.sbmlCompartment="chloroplast";
  F6P_ch.sbmlRole="species";
  F6P_ch.sbmlCompartment="chloroplast";
  E4P_ch.sbmlRole="species";
  E4P_ch.sbmlCompartment="chloroplast";
  X5P_ch.sbmlRole="species";
  X5P_ch.sbmlCompartment="chloroplast";
  SBP_ch.sbmlRole="species";
  SBP_ch.sbmlCompartment="chloroplast";
  S7P_ch.sbmlRole="species";
  S7P_ch.sbmlCompartment="chloroplast";
  R5P_ch.sbmlRole="species";
  R5P_ch.sbmlCompartment="chloroplast";
  Ru5P_ch.sbmlRole="species";
  Ru5P_ch.sbmlCompartment="chloroplast";
  x_Pi_cyt.sbmlRole="species";
  x_Pi_cyt.sbmlCompartment="cytosol";
  x_GAP_cyt.sbmlRole="species";
  x_GAP_cyt.sbmlCompartment="cytosol";
  G6P_ch.sbmlRole="species";
  G6P_ch.sbmlCompartment="chloroplast";
  x_NADP_ch.sbmlRole="species";
  x_NADP_ch.sbmlCompartment="chloroplast";
  x_PGA_cyt.sbmlRole="species";
  x_PGA_cyt.sbmlCompartment="cytosol";
  ADP_ch.sbmlRole="species";
  ADP_ch.sbmlCompartment="chloroplast";
  x_DHAP_cyt.sbmlRole="species";
  x_DHAP_cyt.sbmlCompartment="cytosol";
  x_Proton_ch.sbmlRole="species";
  x_Proton_ch.sbmlCompartment="chloroplast";
  G1P_ch.sbmlRole="species";
  G1P_ch.sbmlCompartment="chloroplast";
  x_Starch_ch.sbmlRole="species";
  x_Starch_ch.sbmlCompartment="chloroplast";
  E1.sbmlRole="rate";
  Rbco_vm.sbmlRole="parameter";
  Rbco_km.sbmlRole="parameter";
  Rbco_KiPGA.sbmlRole="parameter";
  Rbco_KiFBP.sbmlRole="parameter";
  Rbco_KiSBP.sbmlRole="parameter";
  Rbco_KiPi.sbmlRole="parameter";
  Rbco_KiNADPH.sbmlRole="parameter";
  E2.sbmlRole="rate";
  PGK_v.sbmlRole="parameter";
  q2.sbmlRole="parameter";
  E3.sbmlRole="rate";
  G3Pdh_v.sbmlRole="parameter";
  q3.sbmlRole="parameter";
  E4.sbmlRole="rate";
  TPI_v.sbmlRole="parameter";
  q4.sbmlRole="parameter";
  E5.sbmlRole="rate";
  F_Aldo_v.sbmlRole="parameter";
  q5.sbmlRole="parameter";
  E6.sbmlRole="rate";
  FBPase_ch_vm.sbmlRole="parameter";
  FBPase_ch_km.sbmlRole="parameter";
  FBPase_ch_KiF6P.sbmlRole="parameter";
  FBPase_ch_KiPi.sbmlRole="parameter";
  E7.sbmlRole="rate";
  F_TKL_v.sbmlRole="parameter";
  q7.sbmlRole="parameter";
  E8.sbmlRole="rate";
  E_Aldo_v.sbmlRole="parameter";
  q8.sbmlRole="parameter";
  E9.sbmlRole="rate";
  SBPase_ch_vm.sbmlRole="parameter";
  SBPase_ch_km.sbmlRole="parameter";
  SBPase_ch_KiPi.sbmlRole="parameter";
  E10.sbmlRole="rate";
  G_TKL_v.sbmlRole="parameter";
  q10.sbmlRole="parameter";
  E11.sbmlRole="rate";
  R5Piso_v.sbmlRole="parameter";
  q11.sbmlRole="parameter";
  E12.sbmlRole="rate";
  X5Pepi_v.sbmlRole="parameter";
  q12.sbmlRole="parameter";
  E13.sbmlRole="rate";
  Ru5Pk_ch_vm.sbmlRole="parameter";
  Ru5Pk_ch_km1.sbmlRole="parameter";
  Ru5Pk_ch_KiPGA.sbmlRole="parameter";
  Ru5Pk_ch_KiRuBP.sbmlRole="parameter";
  Ru5Pk_ch_KiPi.sbmlRole="parameter";
  Ru5Pk_ch_KiADP1.sbmlRole="parameter";
  Ru5Pk_ch_km2.sbmlRole="parameter";
  Ru5Pk_ch_KiADP2.sbmlRole="parameter";
  E14.sbmlRole="rate";
  PGI_v.sbmlRole="parameter";
  q14.sbmlRole="parameter";
  E15.sbmlRole="rate";
  PGM_v.sbmlRole="parameter";
  q15.sbmlRole="parameter";
  light_reaction.sbmlRole="rate";
  LR_vm.sbmlRole="parameter";
  LR_kmADP.sbmlRole="parameter";
  LR_kmPi.sbmlRole="parameter";
  E16.sbmlRole="rate";
  StSyn_vm.sbmlRole="parameter";
  stsyn_ch_km1.sbmlRole="parameter";
  stsyn_ch_Ki.sbmlRole="parameter";
  stsyn_ch_km2.sbmlRole="parameter";
  stsyn_ch_ka1.sbmlRole="parameter";
  stsyn_ch_ka2.sbmlRole="parameter";
  stsyn_ch_ka3.sbmlRole="parameter";
  E17.sbmlRole="rate";
  StPase_Vm.sbmlRole="parameter";
  StPase_km.sbmlRole="parameter";
  StPase_kiG1P.sbmlRole="parameter";
  E18_DHAP.sbmlRole="rate";
  TP_Piap_vm.sbmlRole="parameter";
  TP_Piap_kDHAP_ch.sbmlRole="parameter";
  TP_Piap_kPi_cyt.sbmlRole="parameter";
  TP_Piap_kPi_ch.sbmlRole="parameter";
  TP_Piap_kPGA_ch.sbmlRole="parameter";
  TP_Piap_kGAP_ch.sbmlRole="parameter";
  E18_PGA.sbmlRole="rate";
  PGA_xpMult.sbmlRole="parameter";
  E18_GAP.sbmlRole="rate";
}