/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000042.xml diagram  at 2008.03.20 15:04:21
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000042 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_ACAflow = compartment*x[0]*flow;
        rate_ADPflow = compartment*(1.1 - x[1])*flow;
        rate_AMPflow = compartment*x[2]*flow;
        rate_ATPflow = compartment*(3.5 - x[3])*flow;
        rate_DPGflow = compartment*x[4]*flow;
        rate_EtOHflow = compartment*x[5]*flow;
        rate_F6Pflow = compartment*x[6]*flow;
        rate_FBPflow = compartment*x[7]*flow;
        rate_GAPflow = compartment*x[8]*flow;
        rate_GLCflow = compartment*(50 - x[9])*flow;
        rate_NADHflow = compartment*(0.24 - x[11])*flow;
        rate_NADflow = compartment*(4.0 - x[10])*flow;
        rate_PEPflow = compartment*x[13]*flow;
        rate_PYRflow = compartment*x[14]*flow;
        rate_Pflow = compartment*x[12]*flow;
        rate_reaction_1 = compartment*(V1*x[3]*x[9]/((K1GLC + x[9])*(K1ATP + x[3])));
        rate_reaction_10 = compartment*k10*x[6];
        rate_reaction_2 = compartment*(V2*x[3]*Math.pow(x[6], 2)/((K2*(1 + k2*Math.pow((x[3]/x[2]), 2)) + Math.pow(x[6], 2))*(K2ATP + x[3])));
        rate_reaction_3 = compartment*(k3f*x[7] - k3b*Math.pow(x[8], 2));
        rate_reaction_4 = compartment*(V4*x[10]*x[8]/((K4GAP + x[8])*(K4NAD + x[10])));
        rate_reaction_5 = compartment*(k5f*x[4]*x[1] - k5b*x[13]*x[3]);
        rate_reaction_6 = compartment*(V6*x[1]*x[13]/((K6PEP + x[13])*(K6ADP + x[1])));
        rate_reaction_7 = compartment*(V7*x[14]/(K7PYR + x[14]));
        rate_reaction_8 = compartment*(k8f*x[11]*x[0] - k8b*x[10]*x[5]);
        rate_reaction_9 = compartment*(k9f*x[2]*x[3] - k9b*Math.pow(x[1], 2));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        compartment = 1.0; // initial value of $compartment
        K1ATP = 0.063; // initial value of K1ATP
        K1GLC = 0.1; // initial value of K1GLC
        K2 = 0.0016; // initial value of K2
        K2ATP = 0.01; // initial value of K2ATP
        K4GAP = 1.0; // initial value of K4GAP
        K4NAD = 1.0; // initial value of K4NAD
        K6ADP = 0.3; // initial value of K6ADP
        K6PEP = 0.2; // initial value of K6PEP
        K7PYR = 0.3; // initial value of K7PYR
        V1 = 0.5; // initial value of V1
        V2 = 1.5; // initial value of V2
        V4 = 10.0; // initial value of V4
        V6 = 10.0; // initial value of V6
        V7 = 2.0; // initial value of V7
        flow = 0.011; // initial value of flow
        k10 = 0.05; // initial value of k10
        k2 = 0.017; // initial value of k2
        k3b = 50.0; // initial value of k3b
        k3f = 1.0; // initial value of k3f
        k5b = 0.5; // initial value of k5b
        k5f = 1.0; // initial value of k5f
        k8b = 1.43E-4; // initial value of k8b
        k8f = 1.0; // initial value of k8f
        k9b = 10.0; // initial value of k9b
        k9f = 10.0; // initial value of k9f
    }

    /*
     * Model variables initial values
     */
    protected double rate_ACAflow;
    protected double rate_ADPflow;
    protected double rate_AMPflow;
    protected double rate_ATPflow;
    protected double rate_DPGflow;
    protected double rate_EtOHflow;
    protected double rate_F6Pflow;
    protected double rate_FBPflow;
    protected double rate_GAPflow;
    protected double rate_GLCflow;
    protected double rate_NADHflow;
    protected double rate_NADflow;
    protected double rate_PEPflow;
    protected double rate_PYRflow;
    protected double rate_Pflow;
    protected double rate_reaction_1;
    protected double rate_reaction_10;
    protected double rate_reaction_2;
    protected double rate_reaction_3;
    protected double rate_reaction_4;
    protected double rate_reaction_5;
    protected double rate_reaction_6;
    protected double rate_reaction_7;
    protected double rate_reaction_8;
    protected double rate_reaction_9;
    protected double compartment;
    protected double K1ATP;
    protected double K1GLC;
    protected double K2;
    protected double K2ATP;
    protected double K4GAP;
    protected double K4NAD;
    protected double K6ADP;
    protected double K6PEP;
    protected double K7PYR;
    protected double V1;
    protected double V2;
    protected double V4;
    protected double V6;
    protected double V7;
    protected double flow;
    protected double k10;
    protected double k2;
    protected double k3b;
    protected double k3f;
    protected double k5b;
    protected double k5f;
    protected double k8b;
    protected double k8f;
    protected double k9b;
    protected double k9f;

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


        double[] y = new double[15];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = x[4];
        y[5] = x[5];
        y[6] = x[6];
        y[7] = x[7];
        y[8] = x[8];
        y[9] = x[9];
        y[10] = x[10];
        y[11] = x[11];
        y[12] = x[12];
        y[13] = x[13];
        y[14] = x[14];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[15];
        this.time = 0.0;
        x[0] = 0.0738334; // - $"compartment.ACA"
        x[1] = 0.108367; // - $"compartment.ADP"
        x[2] = 0.00261149; // - $"compartment.AMP"
        x[3] = 4.49064; // - $"compartment.ATP"
        x[4] = 0.299109; // - $"compartment.DPG"
        x[5] = 0.33981; // - $"compartment.EtOH"
        x[6] = 0.65939; // - $"compartment.F6P"
        x[7] = 0.00770135; // - $"compartment.FBP"
        x[8] = 0.00190919; // - $"compartment.GAP"
        x[9] = 0.0112817; // - $"compartment.GLC"
        x[10] = 3.62057; // - $"compartment.NAD"
        x[11] = 0.616118; // - $"compartment.NADH"
        x[12] = 0.0; // - $"compartment.P"
        x[13] = 0.0021125; // - $"compartment.PEP"
        x[14] = 0.00422702; // - $"compartment.PYR"

        __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 'BIOMD0000000042.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_ACAflow+rate_reaction_7-rate_reaction_8;
        result[1] = +rate_ADPflow+rate_reaction_1+rate_reaction_2-rate_reaction_5-rate_reaction_6+rate_reaction_9*2;
        result[2] = -rate_AMPflow-rate_reaction_9;
        result[3] = +rate_ATPflow-rate_reaction_1-rate_reaction_2+rate_reaction_5+rate_reaction_6-rate_reaction_9;
        result[4] = -rate_DPGflow+rate_reaction_4-rate_reaction_5;
        result[5] = -rate_EtOHflow+rate_reaction_8;
        result[6] = -rate_F6Pflow-rate_reaction_10+rate_reaction_1-rate_reaction_2;
        result[7] = -rate_FBPflow+rate_reaction_2-rate_reaction_3;
        result[8] = -rate_GAPflow+rate_reaction_3*2-rate_reaction_4;
        result[9] = +rate_GLCflow-rate_reaction_1;
        result[10] = +rate_NADflow-rate_reaction_4+rate_reaction_8;
        result[11] = +rate_NADHflow+rate_reaction_4-rate_reaction_8;
        result[12] = -rate_Pflow+rate_reaction_10;
        result[13] = -rate_PEPflow+rate_reaction_5-rate_reaction_6;
        result[14] = -rate_PYRflow+rate_reaction_6-rate_reaction_7;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[15];
        __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 ...