/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000046.xml diagram  at 2008.03.20 15:04:25
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000046 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_v1 = compartment*v1_k1*x[2]*x[11];
        rate_v10 = compartment*v10_k10*x[8]*x[3];
        rate_v11 = compartment*v11_k11*x[7]*x[11];
        rate_v12 = compartment*v12_k12;
        rate_v131 = compartment*v131_k13f*_compartment_O2g_;
        rate_v132 = compartment*v132_k13b*x[11];
        rate_v14 = compartment*v14_k14*x[10]*x[2];
        rate_v2 = compartment*v2_k2*x[1]*x[8];
        rate_v3 = compartment*v3_k3*x[4]*x[0];
        rate_v4 = compartment*v4_k4*x[5]*x[0];
        rate_v5 = compartment*v5_k5*x[3]*x[11];
        rate_v6 = compartment*v6_k6*x[9]*x[8];
        rate_v7 = compartment*v7_k7*x[9]*x[9];
        rate_v8 = compartment*v8_k8*x[6]*x[3];
        rate_v9 = compartment*v9_k9*x[3]*x[3];
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _compartment_O2g_ = 12.0; // initial value of $"compartment.O2g"
        compartment = 1.0; // initial value of $compartment
        v10_k10 = 1.8; // initial value of v10_k10
        v11_k11 = 0.1; // initial value of v11_k11
        v12_k12 = 0.08; // initial value of v12_k12
        v131_k13f = 0.0060; // initial value of v131_k13f
        v132_k13b = 0.0060; // initial value of v132_k13b
        v14_k14 = 0.7; // initial value of v14_k14
        v1_k1 = 3.0E-6; // initial value of v1_k1
        v2_k2 = 18.0; // initial value of v2_k2
        v3_k3 = 0.15; // initial value of v3_k3
        v4_k4 = 0.0052; // initial value of v4_k4
        v5_k5 = 20.0; // initial value of v5_k5
        v6_k6 = 17.0; // initial value of v6_k6
        v7_k7 = 20.0; // initial value of v7_k7
        v8_k8 = 40.0; // initial value of v8_k8
        v9_k9 = 60.0; // initial value of v9_k9
    }

    /*
     * Model variables initial values
     */
    protected double _compartment_NAD_;
    protected double _compartment_NAD2_;
    protected double _compartment_NADHres_;
    protected double _compartment_O2g_;
    protected double rate_v1;
    protected double rate_v10;
    protected double rate_v11;
    protected double rate_v12;
    protected double rate_v131;
    protected double rate_v132;
    protected double rate_v14;
    protected double rate_v2;
    protected double rate_v3;
    protected double rate_v4;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double compartment;
    protected double v10_k10;
    protected double v11_k11;
    protected double v12_k12;
    protected double v131_k13f;
    protected double v132_k13b;
    protected double v14_k14;
    protected double v1_k1;
    protected double v2_k2;
    protected double v3_k3;
    protected double v4_k4;
    protected double v5_k5;
    protected double v6_k6;
    protected double v7_k7;
    protected double v8_k8;
    protected double v9_k9;

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


        double[] y = new double[12];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[12];
        this.time = 0.0;
        x[0] = 500.0; // - $"compartment.ArH"
        x[1] = 0.0; // - $"compartment.H2O2"
        x[2] = 0.0; // - $"compartment.NADH"
        x[3] = 0.0; // - $"compartment.NADrad"
        x[4] = 0.0; // - $"compartment.coI"
        x[5] = 0.0; // - $"compartment.coII"
        x[6] = 0.0; // - $"compartment.coIII"
        x[7] = 0.0; // - $"compartment.per2"
        x[8] = 1.4; // - $"compartment.per3"
        x[9] = 0.0; // - $"compartment.super"
        x[10] = 0.0; // - $compartment.Ar
        x[11] = 0.0; // - $compartment.O2

        __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 'BIOMD0000000046.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_v14-rate_v3-rate_v4;
        result[1] = +rate_v1-rate_v2+rate_v7;
        result[2] = +rate_v12-rate_v14-rate_v1;
        result[3] = -rate_v10+rate_v14-rate_v5-rate_v8-rate_v9*2;
        result[4] = +rate_v2-rate_v3+rate_v8;
        result[5] = +rate_v3-rate_v4;
        result[6] = +rate_v11+rate_v6-rate_v8;
        result[7] = +rate_v10-rate_v11;
        result[8] = -rate_v10-rate_v2+rate_v4-rate_v6;
        result[9] = +rate_v5-rate_v6-rate_v7*2;
        result[10] = -rate_v14+rate_v3+rate_v4;
        result[11] = -rate_v11+rate_v131-rate_v132-rate_v1-rate_v5+rate_v7;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[12];
        __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 ...