/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000045.xml diagram  at 2008.03.20 15:04:24
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000045 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_v2i = _extracellular_cytosol_intravesicular2_*v2i_Vm2i*Math.pow(x[0], 2)/(Math.pow(v2i_K2i, 2) + Math.pow(x[0], 2));
        rate_v2s = _extracellular_cytosol_intravesicular1_*v2s_Vm2s*Math.pow(x[0], 2)/(Math.pow(v2s_K2s, 2) + Math.pow(x[0], 2));
        rate_v3i = _extracellular_cytosol_*v3i_Vm3i*Math.pow(x[2], 2)*Math.pow(x[0], 2)/((Math.pow(v3i_K3y, 2) + Math.pow(x[2], 2))*(Math.pow(v3i_K3z, 2) + Math.pow(x[0], 2)));
        rate_v3s = _extracellular_cytosol_*beta*v3s_Vm3s*Math.pow(x[1], 2)/(Math.pow(v3s_K3s, 2) + Math.pow(x[1], 2));
        rate_v4 = _extracellular_cytosol_*v4_Kf*x[2];
        rate_v5 = extracellular*v5_K*x[0];
        rate_v6 = _extracellular_cytosol_*v6_Kf*x[1];
        rate_vin = _extracellular_cytosol_*(vin_v0 + vin_v1*beta);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _extracellular_cytosol_ = 1.0; // initial value of $"extracellular.cytosol"
        _extracellular_cytosol_intravesicular1_ = 1.0; // initial value of $"extracellular.cytosol.intravesicular1"
        _extracellular_cytosol_intravesicular2_ = 1.0; // initial value of $"extracellular.cytosol.intravesicular2"
        extracellular = 1.0; // initial value of $extracellular
        beta = 1.0; // initial value of beta
        v2i_K2i = 0.0050; // initial value of v2i_K2i
        v2i_Vm2i = 3.1; // initial value of v2i_Vm2i
        v2s_K2s = 0.0265; // initial value of v2s_K2s
        v2s_Vm2s = 1.5; // initial value of v2s_Vm2s
        v3i_K3y = 0.065; // initial value of v3i_K3y
        v3i_K3z = 0.022; // initial value of v3i_K3z
        v3i_Vm3i = 25.0; // initial value of v3i_Vm3i
        v3s_K3s = 0.1; // initial value of v3s_K3s
        v3s_Vm3s = 0.169; // initial value of v3s_Vm3s
        v4_Kf = 0.5; // initial value of v4_Kf
        v5_K = 1.0; // initial value of v5_K
        v6_Kf = 0.5; // initial value of v6_Kf
        vin_v0 = 0.015; // initial value of vin_v0
        vin_v1 = 0.012; // initial value of vin_v1
    }

    /*
     * Model variables initial values
     */
    protected double _extracellular_cytosol_;
    protected double _extracellular_cytosol_intravesicular1_;
    protected double _extracellular_cytosol_intravesicular2_;
    protected double rate_v2i;
    protected double rate_v2s;
    protected double rate_v3i;
    protected double rate_v3s;
    protected double rate_v4;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_vin;
    protected double extracellular;
    protected double beta;
    protected double v2i_K2i;
    protected double v2i_Vm2i;
    protected double v2s_K2s;
    protected double v2s_Vm2s;
    protected double v3i_K3y;
    protected double v3i_K3z;
    protected double v3i_Vm3i;
    protected double v3s_K3s;
    protected double v3s_Vm3s;
    protected double v4_Kf;
    protected double v5_K;
    protected double v6_Kf;
    protected double vin_v0;
    protected double vin_v1;

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


        double[] y = new double[4];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[4];
        this.time = 0.0;
        x[0] = 0.0; // - $"extracellular.cytosol.Z"
        x[1] = 0.5; // - $"extracellular.cytosol.intravesicular1.X"
        x[2] = 0.0; // - $"extracellular.cytosol.intravesicular2.Y"
        x[3] = 0.0; // - $extracellular.EC

        __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 'BIOMD0000000045.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v2i-rate_v2s+rate_v3i+rate_v3s+rate_v4-rate_v5+rate_v6+rate_vin;
        result[1] = +rate_v2s-rate_v3s-rate_v6;
        result[2] = +rate_v2i-rate_v3i-rate_v4;
        result[3] = +rate_v5-rate_vin;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[4];
        __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 ...