/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000039.xml diagram  at 2008.03.20 15:04:18
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000039 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 = Cytosol*(v1_Kch*Math.pow(x[1], 2)*(x[2] - x[1])/(Math.pow(v1_K1, 2) + Math.pow(x[1], 2)));
        rate_v11 = Cytosol*v11_Kminus*x[0];
        rate_v12 = Cytosol*v12_Kplus*x[1]*x[4];
        rate_v3 = Cytosol*v3_Kleak*(x[2] - x[1]);
        rate_v5 = _Cytosol_Endoplasmic_Reticulum_*v5_Kpump*x[1];
        rate_v7 = Cytosol*x[3]*(v7_Kout*Math.pow(x[1], 2)/(Math.pow(v7_K3, 2) + Math.pow(x[1], 2)) + v7_Km);
        rate_v9 = _Cytosol_Mitochondria_*(v9_Kin*Math.pow(x[1], 8)/(Math.pow(v9_K2, 8) + Math.pow(x[1], 8)));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _Cytosol_Endoplasmic_Reticulum_ = 1.0; // initial value of $"Cytosol.Endoplasmic_Reticulum"
        _Cytosol_Mitochondria_ = 1.0; // initial value of $"Cytosol.Mitochondria"
        Cytosol = 1.0; // initial value of $Cytosol
        v11_Kminus = 0.01; // initial value of v11_Kminus
        v12_Kplus = 0.1; // initial value of v12_Kplus
        v1_K1 = 5.0; // initial value of v1_K1
        v1_Kch = 4100.0; // initial value of v1_Kch
        v3_Kleak = 0.05; // initial value of v3_Kleak
        v5_Kpump = 20.0; // initial value of v5_Kpump
        v7_K3 = 5.0; // initial value of v7_K3
        v7_Km = 0.00625; // initial value of v7_Km
        v7_Kout = 125.0; // initial value of v7_Kout
        v9_K2 = 0.8; // initial value of v9_K2
        v9_Kin = 300.0; // initial value of v9_Kin
    }

    /*
     * Model variables initial values
     */
    protected double _Cytosol_Endoplasmic_Reticulum_;
    protected double _Cytosol_Mitochondria_;
    protected double rate_v1;
    protected double rate_v11;
    protected double rate_v12;
    protected double rate_v3;
    protected double rate_v5;
    protected double rate_v7;
    protected double rate_v9;
    protected double Cytosol;
    protected double v11_Kminus;
    protected double v12_Kplus;
    protected double v1_K1;
    protected double v1_Kch;
    protected double v3_Kleak;
    protected double v5_Kpump;
    protected double v7_K3;
    protected double v7_Km;
    protected double v7_Kout;
    protected double v9_K2;
    protected double v9_Kin;

    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] = 85.45; // - $"Cytosol.CaPr"
        x[1] = 0.35; // - $"Cytosol.Ca_cyt"
        x[2] = 0.76; // - $"Cytosol.Endoplasmic_Reticulum.CaER"
        x[3] = 0.29; // - $"Cytosol.Mitochondria.CaM"
        x[4] = 34.55; // - $Cytosol.Pr

        __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 'BIOMD0000000039.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v11+rate_v12;
        result[1] = +rate_v11-rate_v12+rate_v1+rate_v3-rate_v5+rate_v7-rate_v9;
        result[2] = -rate_v1*0.25-rate_v3*0.25+rate_v5*0.25;
        result[3] = -rate_v7*0.25+rate_v9*0.25;
        result[4] = +rate_v11-rate_v12;
    }
    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 ...