/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000063.xml diagram  at 2008.03.20 15:04:48
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000063 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_Vatpase = Vatpase_Vm8*x[0];
        rate_Vgapd = Vgapd_Vm5/(1 + Vgapd_K5G3P/(0.01*x[1]) + (Vgapd_K5NAD/Vgapd_NAD + Vgapd_K5G3P*Vgapd_K5NAD/(Vgapd_NAD*0.01*x[1]) + Vgapd_K5G3P*Vgapd_K5NAD*Vgapd_NADH/(Vgapd_NAD*0.01*x[1]*Vgapd_K5NADH))*(1 + 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgapd_K5ADP + (3 - x[0] - 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5)))/Vgapd_K5AMP + x[0]/Vgapd_K5ATP));
        rate_Vgol = Vgol_Vm7*(x[4]/Vgol_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP)*(Vgol_g6R*(1 + x[4]/Vgol_K6PEP + 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP + Vgol_g6R*x[4]/Vgol_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP) + Vgol_q6*Vgol_L60*Math.pow(((1 + Vgol_c6FDP*x[1]/Vgol_K6FDP)/(1 + x[1]/Vgol_K6FDP)), 2)*Vgol_g6T*Vgol_c6PEP*x[4]/Vgol_K6PEP*Vgol_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP*(1 + Vgol_c6PEP*x[4]/Vgol_K6PEP + Vgol_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP + Vgol_g6T*Vgol_c6PEP*x[4]/Vgol_K6PEP*Vgol_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP))/((1 + 9.550000000000001E-9/Vgol_h6)*(Math.pow((1 + x[4]/Vgol_K6PEP + 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP + Vgol_g6R*x[4]/Vgol_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP), 2) + Vgol_L60*Math.pow(((1 + Vgol_c6FDP*x[1]/Vgol_K6FDP)/(1 + x[1]/Vgol_K6FDP)), 2)*Math.pow((1 + Vgol_c6PEP*x[4]/Vgol_K6PEP + Vgol_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP + Vgol_g6T*Vgol_c6PEP*x[4]/Vgol_K6PEP*Vgol_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vgol_K6ADP), 2)));
        rate_Vhk = Vhk_Vm2/(1 + Vhk_Km2Glc/x[3] + Vhk_Km2ATP/x[0] + Vhk_Ks2Glc*Vhk_Km2ATP/(x[3]*x[0]));
        rate_Vin = Vin_Vm1 - Vin_Ki1G6P*x[2];
        rate_Vpfk = Vpfk_Vm4*Vpfk_g4R*0.3*x[2]/Vpfk_K4F6P*x[0]/Vpfk_K4ATP*(1 + 0.3*x[2]/Vpfk_K4F6P + x[0]/Vpfk_K4ATP + Vpfk_g4R*0.3*x[2]/Vpfk_K4F6P*x[0]/Vpfk_K4ATP)/(Math.pow((1 + 0.3*x[2]/Vpfk_K4F6P + x[0]/Vpfk_K4ATP + Vpfk_g4R*0.3*x[2]/Vpfk_K4F6P*x[0]/Vpfk_K4ATP), 2) + Vpfk_L40*Math.pow(((1 + Vpfk_c4AMP*(3 - x[0] - 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5)))/Vpfk_K4AMP)/(1 + (3 - x[0] - 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5)))/Vpfk_K4AMP)), 2)*Math.pow((1 + Vpfk_c4F6P*0.3*x[2]/Vpfk_K4F6P + Vpfk_c4ATP*x[0]/Vpfk_K4ATP + Vpfk_gT*Vpfk_c4F6P*0.3*x[2]/Vpfk_K4F6P*Vpfk_c4ATP*x[0]/Vpfk_K4ATP), 2));
        rate_Vpk = Vpk_Vm6*(x[4]/Vpk_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP)*(Vpk_g6R*(1 + x[4]/Vpk_K6PEP + 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP + Vpk_g6R*x[4]/Vpk_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP) + Vpk_q6*Vpk_L60*Math.pow(((1 + Vpk_c6FDP*x[1]/Vpk_K6FDP)/(1 + x[1]/Vpk_K6FDP)), 2)*Vpk_g6T*Vpk_c6PEP*x[4]/Vpk_K6PEP*Vpk_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP*(1 + Vpk_c6PEP*x[4]/Vpk_K6PEP + Vpk_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP + Vpk_g6T*Vpk_c6PEP*x[4]/Vpk_K6PEP*Vpk_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP))/((1 + 9.550000000000001E-9/Vpk_h6)*(Math.pow((1 + x[4]/Vpk_K6PEP + 0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP + Vpk_g6R*x[4]/Vpk_K6PEP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP), 2) + Vpk_L60*Math.pow(((1 + Vpk_c6FDP*x[1]/Vpk_K6FDP)/(1 + x[1]/Vpk_K6FDP)), 2)*Math.pow((1 + Vpk_c6PEP*x[4]/Vpk_K6PEP + Vpk_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP + Vpk_g6T*Vpk_c6PEP*x[4]/Vpk_K6PEP*Vpk_c6ADP*0.5*(-x[0] + Math.pow((12*x[0] - 3*Math.pow(x[0], 2)), 0.5))/Vpk_K6ADP), 2)));
        rate_Vpol = 1.1*Vpol_Vm3*Math.pow(x[2], Vpol_n3)/(Math.pow(Vpol_K3Gly, Vpol_n3) + Math.pow(x[2], Vpol_n3))/(1 + Vpol_Km30/0.7*(1 + Vpol_Km3G6P/x[2]));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _extracellular_Glco_ = 1.0; // initial value of $"extracellular.Glco"
        Vatpase_Vm8 = 25.1; // initial value of Vatpase_Vm8
        Vgapd_K5ADP = 1.5; // initial value of Vgapd_K5ADP
        Vgapd_K5AMP = 1.1; // initial value of Vgapd_K5AMP
        Vgapd_K5ATP = 2.5; // initial value of Vgapd_K5ATP
        Vgapd_K5G3P = 0.0025; // initial value of Vgapd_K5G3P
        Vgapd_K5NAD = 0.18; // initial value of Vgapd_K5NAD
        Vgapd_K5NADH = 3.0E-4; // initial value of Vgapd_K5NADH
        Vgapd_NAD = 1.91939; // initial value of Vgapd_NAD
        Vgapd_NADH = 0.0806142; // initial value of Vgapd_NADH
        Vgapd_Vm5 = 49.9; // initial value of Vgapd_Vm5
        Vgol_K6ADP = 5.0; // initial value of Vgol_K6ADP
        Vgol_K6FDP = 0.2; // initial value of Vgol_K6FDP
        Vgol_K6PEP = 0.00793966; // initial value of Vgol_K6PEP
        Vgol_L60 = 164.084; // initial value of Vgol_L60
        Vgol_Vm7 = 203.0; // initial value of Vgol_Vm7
        Vgol_c6ADP = 1.0; // initial value of Vgol_c6ADP
        Vgol_c6FDP = 0.01; // initial value of Vgol_c6FDP
        Vgol_c6PEP = 1.58793E-4; // initial value of Vgol_c6PEP
        Vgol_g6R = 0.1; // initial value of Vgol_g6R
        Vgol_g6T = 1.0; // initial value of Vgol_g6T
        Vgol_h6 = 1.14815E-7; // initial value of Vgol_h6
        Vgol_q6 = 1.0; // initial value of Vgol_q6
        Vhk_Km2ATP = 0.1; // initial value of Vhk_Km2ATP
        Vhk_Km2Glc = 0.11; // initial value of Vhk_Km2Glc
        Vhk_Ks2Glc = 0.0062; // initial value of Vhk_Ks2Glc
        Vhk_Vm2 = 68.5; // initial value of Vhk_Vm2
        Vin_Ki1G6P = 3.7; // initial value of Vin_Ki1G6P
        Vin_Vm1 = 19.7; // initial value of Vin_Vm1
        Vpfk_K4AMP = 0.025; // initial value of Vpfk_K4AMP
        Vpfk_K4ATP = 0.06; // initial value of Vpfk_K4ATP
        Vpfk_K4F6P = 1.0; // initial value of Vpfk_K4F6P
        Vpfk_L40 = 3342.0; // initial value of Vpfk_L40
        Vpfk_Vm4 = 31.7; // initial value of Vpfk_Vm4
        Vpfk_c4AMP = 0.019; // initial value of Vpfk_c4AMP
        Vpfk_c4ATP = 1.0; // initial value of Vpfk_c4ATP
        Vpfk_c4F6P = 5.0E-4; // initial value of Vpfk_c4F6P
        Vpfk_g4R = 10.0; // initial value of Vpfk_g4R
        Vpfk_gT = 1.0; // initial value of Vpfk_gT
        Vpk_K6ADP = 5.0; // initial value of Vpk_K6ADP
        Vpk_K6FDP = 0.2; // initial value of Vpk_K6FDP
        Vpk_K6PEP = 0.00793966; // initial value of Vpk_K6PEP
        Vpk_L60 = 164.084; // initial value of Vpk_L60
        Vpk_Vm6 = 3440.0; // initial value of Vpk_Vm6
        Vpk_c6ADP = 1.0; // initial value of Vpk_c6ADP
        Vpk_c6FDP = 0.01; // initial value of Vpk_c6FDP
        Vpk_c6PEP = 1.58793E-4; // initial value of Vpk_c6PEP
        Vpk_g6R = 0.1; // initial value of Vpk_g6R
        Vpk_g6T = 1.0; // initial value of Vpk_g6T
        Vpk_h6 = 1.14815E-7; // initial value of Vpk_h6
        Vpk_q6 = 1.0; // initial value of Vpk_q6
        Vpol_K3Gly = 2.0; // initial value of Vpol_K3Gly
        Vpol_Km30 = 1.0; // initial value of Vpol_Km30
        Vpol_Km3G6P = 1.1; // initial value of Vpol_Km3G6P
        Vpol_Vm3 = 14.31; // initial value of Vpol_Vm3
        Vpol_n3 = 8.25; // initial value of Vpol_n3
    }

    /*
     * Model variables initial values
     */
    protected double _extracellular_Glco_;
    protected double _extracellular_cytoplasm_Carbo_;
    protected double _extracellular_cytoplasm_EtOH_;
    protected double _extracellular_cytoplasm_Gly_;
    protected double rate_Vatpase;
    protected double rate_Vgapd;
    protected double rate_Vgol;
    protected double rate_Vhk;
    protected double rate_Vin;
    protected double rate_Vpfk;
    protected double rate_Vpk;
    protected double rate_Vpol;
    protected double Vatpase_Vm8;
    protected double Vgapd_K5ADP;
    protected double Vgapd_K5AMP;
    protected double Vgapd_K5ATP;
    protected double Vgapd_K5G3P;
    protected double Vgapd_K5NAD;
    protected double Vgapd_K5NADH;
    protected double Vgapd_NAD;
    protected double Vgapd_NADH;
    protected double Vgapd_Vm5;
    protected double Vgol_K6ADP;
    protected double Vgol_K6FDP;
    protected double Vgol_K6PEP;
    protected double Vgol_L60;
    protected double Vgol_Vm7;
    protected double Vgol_c6ADP;
    protected double Vgol_c6FDP;
    protected double Vgol_c6PEP;
    protected double Vgol_g6R;
    protected double Vgol_g6T;
    protected double Vgol_h6;
    protected double Vgol_q6;
    protected double Vhk_Km2ATP;
    protected double Vhk_Km2Glc;
    protected double Vhk_Ks2Glc;
    protected double Vhk_Vm2;
    protected double Vin_Ki1G6P;
    protected double Vin_Vm1;
    protected double Vpfk_K4AMP;
    protected double Vpfk_K4ATP;
    protected double Vpfk_K4F6P;
    protected double Vpfk_L40;
    protected double Vpfk_Vm4;
    protected double Vpfk_c4AMP;
    protected double Vpfk_c4ATP;
    protected double Vpfk_c4F6P;
    protected double Vpfk_g4R;
    protected double Vpfk_gT;
    protected double Vpk_K6ADP;
    protected double Vpk_K6FDP;
    protected double Vpk_K6PEP;
    protected double Vpk_L60;
    protected double Vpk_Vm6;
    protected double Vpk_c6ADP;
    protected double Vpk_c6FDP;
    protected double Vpk_c6PEP;
    protected double Vpk_g6R;
    protected double Vpk_g6T;
    protected double Vpk_h6;
    protected double Vpk_q6;
    protected double Vpol_K3Gly;
    protected double Vpol_Km30;
    protected double Vpol_Km3G6P;
    protected double Vpol_Vm3;
    protected double Vpol_n3;

    public double[] extendResult(double time,double [] x)
    {
        this.time = time;


        double[] y = new double[5];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = x[4];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[5];
        this.time = 0.0;
        x[0] = 1.19; // - $"extracellular.cytoplasm.ATP"
        x[1] = 9.144; // - $"extracellular.cytoplasm.FDP"
        x[2] = 1.011; // - $"extracellular.cytoplasm.G6P"
        x[3] = 0.0345; // - $"extracellular.cytoplasm.Glci"
        x[4] = 0.0095; // - $"extracellular.cytoplasm.PEP"

        __internalRateVarInitFunc_0(time, x);

        return x;
    }

/*
 * code for algebraic rules calculations
 */

/*
 * end of code for algebraic rules calculations
 */

    protected void calculateRates(double time, double[] x)
    {

        __internalRateVarInitFunc_0(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000063.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Vatpase+rate_Vgapd*2-rate_Vhk-rate_Vpfk+rate_Vpk-rate_Vpol;
        result[1] = -rate_Vgapd-rate_Vgol*0.5+rate_Vpfk;
        result[2] = +rate_Vhk-rate_Vpfk-rate_Vpol;
        result[3] = -rate_Vhk+rate_Vin;
        result[4] = +rate_Vgapd*2-rate_Vpk;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[5];
        __internalDyDt_0(time, x, result);
        return result;
    }
    public double[] dy_dt(double time, double[] x)
    {
        this.time = time;
        calculateRates( time,x );

        return calculateResult( time,x );
    }

} // class ...