/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000123.xml diagram  at 2008.03.20 15:09:00
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000123 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_R1 = _cytosol_nucleus_*(k1*(x[13]/_cytosol_nucleus_) - k2*(x[11]/_cytosol_nucleus_));
        rate_R10 = cytosol*k3*(x[6]/cytosol) - _cytosol_nucleus_*k4*(x[13]/_cytosol_nucleus_);
        rate_R11 = cytosol*(k15*(x[3]/cytosol) - k16*(x[4]/cytosol)*(x[0]/cytosol));
        rate_R12 = cytosol*(k1*(x[6]/cytosol) - k2*(x[4]/cytosol));
        rate_R13 = cytosol*(k19*(x[2]/cytosol)*Math.pow((x[1]/cytosol), 3) - k20*(x[0]/cytosol));
        rate_R14 = _cytosol_nucleus_*(k19*(x[9]/_cytosol_nucleus_)*Math.pow((x[8]/_cytosol_nucleus_), 3) - k20*(x[7]/_cytosol_nucleus_));
        rate_R15 = cytosol*k5*(x[2]/cytosol) - _cytosol_nucleus_*k6*(x[9]/_cytosol_nucleus_);
        rate_R16 = cytosol*k21*(x[1]/cytosol) - _cytosol_nucleus_*k22*(x[8]/_cytosol_nucleus_);
        rate_R17 = cytosol*k7*(x[5]/cytosol) - _cytosol_nucleus_*k8*(x[12]/_cytosol_nucleus_);
        rate_R2 = _cytosol_nucleus_*(k16*(x[11]/_cytosol_nucleus_)*(x[7]/_cytosol_nucleus_) - k15*(x[10]/_cytosol_nucleus_));
        rate_R3 = _cytosol_nucleus_*k18*(x[11]/_cytosol_nucleus_) - cytosol*k17*(x[4]/cytosol);
        rate_R4 = _cytosol_nucleus_*k6*(x[7]/_cytosol_nucleus_) - cytosol*k5*(x[0]/cytosol);
        rate_R5 = _cytosol_nucleus_*(k14*(x[10]/_cytosol_nucleus_) - k13*(x[12]/_cytosol_nucleus_));
        rate_R6 = _cytosol_nucleus_*(k12*(x[12]/_cytosol_nucleus_) - k11*(x[13]/_cytosol_nucleus_)*(x[7]/_cytosol_nucleus_));
        rate_R7 = _cytosol_nucleus_*k10*(x[10]/_cytosol_nucleus_) - cytosol*k9*(x[3]/cytosol);
        rate_R8 = cytosol*(k14*(x[3]/cytosol) - k13*(x[5]/cytosol));
        rate_R9 = cytosol*(k12*(x[5]/cytosol) - k11*(x[6]/cytosol)*(x[0]/cytosol));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _cytosol_nucleus_ = 1.13E-13; // initial value of $"cytosol.nucleus"
        cytosol = 2.69E-13; // initial value of $cytosol
        k1 = 2.56E-5; // initial value of k1
        k10 = 0.0050; // initial value of k10
        k11 = 6.63; // initial value of k11
        k12 = 0.00168; // initial value of k12
        k13 = 0.5; // initial value of k13
        k14 = 0.00256; // initial value of k14
        k15 = 0.00168; // initial value of k15
        k16 = 6.63; // initial value of k16
        k17 = 0.0015; // initial value of k17
        k18 = 9.6E-4; // initial value of k18
        k19 = 1.0; // initial value of k19
        k2 = 0.00256; // initial value of k2
        k20 = 1.0; // initial value of k20
        k21 = 0.21; // initial value of k21
        k22 = 0.5; // initial value of k22
        k3 = 0.0050; // initial value of k3
        k4 = 0.5; // initial value of k4
        k5 = 0.0019; // initial value of k5
        k6 = 9.2E-4; // initial value of k6
        k7 = 0.0050; // initial value of k7
        k8 = 0.5; // initial value of k8
        k9 = 0.5; // initial value of k9
    }

    /*
     * Model variables initial values
     */
    protected double _cytosol_nucleus_;
    protected double rate_R1;
    protected double rate_R10;
    protected double rate_R11;
    protected double rate_R12;
    protected double rate_R13;
    protected double rate_R14;
    protected double rate_R15;
    protected double rate_R16;
    protected double rate_R17;
    protected double rate_R2;
    protected double rate_R3;
    protected double rate_R4;
    protected double rate_R5;
    protected double rate_R6;
    protected double rate_R7;
    protected double rate_R8;
    protected double rate_R9;
    protected double cytosol;
    protected double k1;
    protected double k10;
    protected double k11;
    protected double k12;
    protected double k13;
    protected double k14;
    protected double k15;
    protected double k16;
    protected double k17;
    protected double k18;
    protected double k19;
    protected double k2;
    protected double k20;
    protected double k21;
    protected double k22;
    protected double k3;
    protected double k4;
    protected double k5;
    protected double k6;
    protected double k7;
    protected double k8;
    protected double k9;

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


        double[] y = new double[14];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[14];
        this.time = 0.0;
        x[0] = 2.4479E-18; // - $"cytosol.Act_C_Cyt"
        x[1] = 2.69E-13; // - $"cytosol.Ca_Cyt"
        x[2] = 2.6122052000000004E-15; // - $"cytosol.Inact_C_Cyt"
        x[3] = 1.6409E-18; // - $"cytosol.NFAT_Act_C_Cyt"
        x[4] = 2.9616900000000005E-17; // - $"cytosol.NFAT_Cyt"
        x[5] = 5.918000000000001E-19; // - $"cytosol.NFAT_Pi_Act_C_Cyt"
        x[6] = 2.5392793000000002E-15; // - $"cytosol.NFAT_Pi_Cyt"
        x[7] = 5.7065E-18; // - $"cytosol.nucleus.Act_C_Nuc"
        x[8] = 1.13E-13; // - $"cytosol.nucleus.Ca_Nuc"
        x[9] = 5.5593739999999995E-15; // - $"cytosol.nucleus.Inact_C_Nuc"
        x[10] = 1.070901E-16; // - $"cytosol.nucleus.NFAT_Act_C_Nuc"
        x[11] = 5.897469999999999E-17; // - $"cytosol.nucleus.NFAT_Nuc"
        x[12] = 2.8250000000000004E-19; // - $"cytosol.nucleus.NFAT_Pi_Act_C_Nuc"
        x[13] = 2.56736E-17; // - $"cytosol.nucleus.NFAT_Pi_Nuc"

        __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 'BIOMD0000000123.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_R11+rate_R12-rate_R12+rate_R13+rate_R4+rate_R9;
        result[1] = -rate_R13*3-rate_R16;
        result[2] = -rate_R13-rate_R15;
        result[3] = -rate_R11+rate_R7-rate_R8;
        result[4] = +rate_R11+rate_R12+rate_R3;
        result[5] = -rate_R17+rate_R8-rate_R9;
        result[6] = -rate_R10-rate_R12+rate_R9;
        result[7] = +rate_R14+rate_R1-rate_R1-rate_R2-rate_R4+rate_R6;
        result[8] = -rate_R14*3+rate_R16;
        result[9] = -rate_R14+rate_R15;
        result[10] = +rate_R2-rate_R5-rate_R7;
        result[11] = +rate_R1-rate_R2-rate_R3;
        result[12] = +rate_R17+rate_R5-rate_R6;
        result[13] = +rate_R10-rate_R1+rate_R6;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[14];
        __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 ...