/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000080.xml diagram  at 2008.03.20 15:08:01
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000080 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_Reaction_1 = cell*(Reaction_1_k1*x[0]*x[8] - Reaction_1_k7*x[9]);
        rate_Reaction_2 = cell*(Reaction_2_k2*x[9]*x[6] - Reaction_2_k8*x[2]);
        rate_Reaction_3 = cell*(Reaction_3_k3*x[2] - Reaction_3_k9*x[4]*x[1]);
        rate_Reaction_4 = cell*(Reaction_4_k4*x[1]*x[5] - Reaction_4_k10*x[3]);
        rate_Reaction_5 = cell*Reaction_5_k5*x[3];
        rate_Reaction_6 = cell*Reaction_6_k6*x[7];
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        cell = 1.0; // initial value of $cell
        Reaction_1_k1 = 5000000.0; // initial value of Reaction_1_k1
        Reaction_1_k7 = 10.0; // initial value of Reaction_1_k7
        Reaction_2_k2 = 1.0E8; // initial value of Reaction_2_k2
        Reaction_2_k8 = 0.1; // initial value of Reaction_2_k8
        Reaction_3_k3 = 5.0; // initial value of Reaction_3_k3
        Reaction_3_k9 = 100000.0; // initial value of Reaction_3_k9
        Reaction_4_k10 = 55.0; // initial value of Reaction_4_k10
        Reaction_4_k4 = 5000000.0; // initial value of Reaction_4_k4
        Reaction_5_k5 = 1.0; // initial value of Reaction_5_k5
        Reaction_6_k6 = 2.0; // initial value of Reaction_6_k6
    }

    /*
     * Model variables initial values
     */
    protected double rate_Reaction_1;
    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 cell;
    protected double Reaction_1_k1;
    protected double Reaction_1_k7;
    protected double Reaction_2_k2;
    protected double Reaction_2_k8;
    protected double Reaction_3_k3;
    protected double Reaction_3_k9;
    protected double Reaction_4_k10;
    protected double Reaction_4_k4;
    protected double Reaction_5_k5;
    protected double Reaction_6_k6;

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


        double[] y = new double[10];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[10];
        this.time = 0.0;
        x[0] = 3.1E-5; // - $"cell.D"
        x[1] = 0.0; // - $"cell.DRG"
        x[2] = 0.0; // - $"cell.DRG_GDP"
        x[3] = 0.0; // - $"cell.DRG_GTP"
        x[4] = 0.0; // - $"cell.GDP"
        x[5] = 1.0E-5; // - $"cell.GTP"
        x[6] = 1.0E-6; // - $"cell.G_GDP"
        x[7] = 0.0; // - $"cell.G_GTP"
        x[8] = 1.0E-10; // - $"cell.R"
        x[9] = 0.0; // - $cell.DR

        __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 'BIOMD0000000080.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Reaction_1;
        result[1] = +rate_Reaction_3-rate_Reaction_4;
        result[2] = +rate_Reaction_2-rate_Reaction_3;
        result[3] = +rate_Reaction_4-rate_Reaction_5;
        result[4] = +rate_Reaction_3;
        result[5] = -rate_Reaction_4;
        result[6] = -rate_Reaction_2+rate_Reaction_6;
        result[7] = +rate_Reaction_5-rate_Reaction_6;
        result[8] = -rate_Reaction_1;
        result[9] = +rate_Reaction_1-rate_Reaction_2+rate_Reaction_5;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[10];
        __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 ...