/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000011.xml diagram  at 2008.03.20 15:03:26
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000011 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_Reaction1 = Reaction1_a1*x[16]*x[17];
        rate_Reaction10 = Reaction10_a4*x[11]*x[9];
        rate_Reaction11 = Reaction11_d4*x[12];
        rate_Reaction12 = Reaction12_k4*x[12];
        rate_Reaction13 = Reaction13_a5*x[11]*x[20];
        rate_Reaction14 = Reaction14_d5*x[13];
        rate_Reaction15 = Reaction15_k5*x[13];
        rate_Reaction16 = Reaction16_a6*x[9]*x[14];
        rate_Reaction17 = Reaction17_d6*x[15];
        rate_Reaction18 = Reaction18_k6*x[15];
        rate_Reaction19 = Reaction19_a7*x[0]*x[14];
        rate_Reaction2 = Reaction2_d1*x[19];
        rate_Reaction20 = Reaction20_d7*x[1];
        rate_Reaction21 = Reaction21_k7*x[1];
        rate_Reaction22 = Reaction22_a8*x[3]*x[2];
        rate_Reaction23 = Reaction23_d8*x[4];
        rate_Reaction24 = Reaction24_k8*x[4];
        rate_Reaction25 = Reaction25_a9*x[3]*x[14];
        rate_Reaction26 = Reaction26_d9*x[5];
        rate_Reaction27 = Reaction27_k9*x[5];
        rate_Reaction28 = Reaction28_a10*x[2]*x[6];
        rate_Reaction29 = Reaction29_d10*x[7];
        rate_Reaction3 = Reaction3_k1*x[19];
        rate_Reaction30 = Reaction30_k10*x[7];
        rate_Reaction4 = Reaction4_a2*x[20]*x[18];
        rate_Reaction5 = Reaction5_d2*x[21];
        rate_Reaction6 = Reaction6_k2*x[21];
        rate_Reaction7 = Reaction7_a3*x[8]*x[20];
        rate_Reaction8 = Reaction8_d3*x[10];
        rate_Reaction9 = Reaction9_k3*x[10];
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        Reaction10_a4 = 10.0; // initial value of Reaction10_a4
        Reaction11_d4 = 0.8; // initial value of Reaction11_d4
        Reaction12_k4 = 0.1; // initial value of Reaction12_k4
        Reaction13_a5 = 3.3; // initial value of Reaction13_a5
        Reaction14_d5 = 0.4; // initial value of Reaction14_d5
        Reaction15_k5 = 0.1; // initial value of Reaction15_k5
        Reaction16_a6 = 10.0; // initial value of Reaction16_a6
        Reaction17_d6 = 0.8; // initial value of Reaction17_d6
        Reaction18_k6 = 0.1; // initial value of Reaction18_k6
        Reaction19_a7 = 20.0; // initial value of Reaction19_a7
        Reaction1_a1 = 1.0; // initial value of Reaction1_a1
        Reaction20_d7 = 0.6; // initial value of Reaction20_d7
        Reaction21_k7 = 0.1; // initial value of Reaction21_k7
        Reaction22_a8 = 5.0; // initial value of Reaction22_a8
        Reaction23_d8 = 0.4; // initial value of Reaction23_d8
        Reaction24_k8 = 0.1; // initial value of Reaction24_k8
        Reaction25_a9 = 20.0; // initial value of Reaction25_a9
        Reaction26_d9 = 0.6; // initial value of Reaction26_d9
        Reaction27_k9 = 0.1; // initial value of Reaction27_k9
        Reaction28_a10 = 5.0; // initial value of Reaction28_a10
        Reaction29_d10 = 0.4; // initial value of Reaction29_d10
        Reaction2_d1 = 0.4; // initial value of Reaction2_d1
        Reaction30_k10 = 0.1; // initial value of Reaction30_k10
        Reaction3_k1 = 0.1; // initial value of Reaction3_k1
        Reaction4_a2 = 0.5; // initial value of Reaction4_a2
        Reaction5_d2 = 0.5; // initial value of Reaction5_d2
        Reaction6_k2 = 0.1; // initial value of Reaction6_k2
        Reaction7_a3 = 3.3; // initial value of Reaction7_a3
        Reaction8_d3 = 0.42; // initial value of Reaction8_d3
        Reaction9_k3 = 0.1; // initial value of Reaction9_k3
    }

    /*
     * Model variables initial values
     */
    protected double rate_Reaction1;
    protected double rate_Reaction10;
    protected double rate_Reaction11;
    protected double rate_Reaction12;
    protected double rate_Reaction13;
    protected double rate_Reaction14;
    protected double rate_Reaction15;
    protected double rate_Reaction16;
    protected double rate_Reaction17;
    protected double rate_Reaction18;
    protected double rate_Reaction19;
    protected double rate_Reaction2;
    protected double rate_Reaction20;
    protected double rate_Reaction21;
    protected double rate_Reaction22;
    protected double rate_Reaction23;
    protected double rate_Reaction24;
    protected double rate_Reaction25;
    protected double rate_Reaction26;
    protected double rate_Reaction27;
    protected double rate_Reaction28;
    protected double rate_Reaction29;
    protected double rate_Reaction3;
    protected double rate_Reaction30;
    protected double rate_Reaction4;
    protected double rate_Reaction5;
    protected double rate_Reaction6;
    protected double rate_Reaction7;
    protected double rate_Reaction8;
    protected double rate_Reaction9;
    protected double Reaction10_a4;
    protected double Reaction11_d4;
    protected double Reaction12_k4;
    protected double Reaction13_a5;
    protected double Reaction14_d5;
    protected double Reaction15_k5;
    protected double Reaction16_a6;
    protected double Reaction17_d6;
    protected double Reaction18_k6;
    protected double Reaction19_a7;
    protected double Reaction1_a1;
    protected double Reaction20_d7;
    protected double Reaction21_k7;
    protected double Reaction22_a8;
    protected double Reaction23_d8;
    protected double Reaction24_k8;
    protected double Reaction25_a9;
    protected double Reaction26_d9;
    protected double Reaction27_k9;
    protected double Reaction28_a10;
    protected double Reaction29_d10;
    protected double Reaction2_d1;
    protected double Reaction30_k10;
    protected double Reaction3_k1;
    protected double Reaction4_a2;
    protected double Reaction5_d2;
    protected double Reaction6_k2;
    protected double Reaction7_a3;
    protected double Reaction8_d3;
    protected double Reaction9_k3;

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


        double[] y = new double[22];
        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];
        y[14] = x[14];
        y[15] = x[15];
        y[16] = x[16];
        y[17] = x[17];
        y[18] = x[18];
        y[19] = x[19];
        y[20] = x[20];
        y[21] = x[21];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[22];
        this.time = 0.0;
        x[0] = 0.3; // - $"Cytoplasm.MAPK"
        x[1] = 0.0; // - $"Cytoplasm.MAPKMEKpp"
        x[2] = 0.3; // - $"Cytoplasm.MAPKPH"
        x[3] = 0.0; // - $"Cytoplasm.MAPKp"
        x[4] = 0.0; // - $"Cytoplasm.MAPKpMAPKPH"
        x[5] = 0.0; // - $"Cytoplasm.MAPKpMEKpp"
        x[6] = 0.0; // - $"Cytoplasm.MAPKpp"
        x[7] = 0.0; // - $"Cytoplasm.MAPKppMAPKPH"
        x[8] = 0.2; // - $"Cytoplasm.MEK"
        x[9] = 0.2; // - $"Cytoplasm.MEKPH"
        x[10] = 0.0; // - $"Cytoplasm.MEKRAFp"
        x[11] = 0.0; // - $"Cytoplasm.MEKp"
        x[12] = 0.0; // - $"Cytoplasm.MEKpMEKPH"
        x[13] = 0.0; // - $"Cytoplasm.MEKpRAFp"
        x[14] = 0.0; // - $"Cytoplasm.MEKpp"
        x[15] = 0.0; // - $"Cytoplasm.MEKppMEKPH"
        x[16] = 0.4; // - $"Cytoplasm.RAF"
        x[17] = 0.1; // - $"Cytoplasm.RAFK"
        x[18] = 0.3; // - $"Cytoplasm.RAFPH"
        x[19] = 0.0; // - $"Cytoplasm.RAFRAFK"
        x[20] = 0.0; // - $"Cytoplasm.RAFp"
        x[21] = 0.0; // - $"Cytoplasm.RAFpRAFPH"

        __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 'BIOMD0000000011.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_Reaction19+rate_Reaction20+rate_Reaction24;
        result[1] = +rate_Reaction19-rate_Reaction20-rate_Reaction21;
        result[2] = -rate_Reaction22+rate_Reaction23+rate_Reaction24-rate_Reaction28+rate_Reaction29+rate_Reaction30;
        result[3] = +rate_Reaction21-rate_Reaction22+rate_Reaction23-rate_Reaction25+rate_Reaction26+rate_Reaction30;
        result[4] = +rate_Reaction22-rate_Reaction23-rate_Reaction24;
        result[5] = +rate_Reaction25-rate_Reaction26-rate_Reaction27;
        result[6] = +rate_Reaction27-rate_Reaction28+rate_Reaction29;
        result[7] = +rate_Reaction28-rate_Reaction29-rate_Reaction30;
        result[8] = +rate_Reaction12-rate_Reaction7+rate_Reaction8;
        result[9] = -rate_Reaction10+rate_Reaction11+rate_Reaction12-rate_Reaction16+rate_Reaction17+rate_Reaction18;
        result[10] = +rate_Reaction7-rate_Reaction8-rate_Reaction9;
        result[11] = -rate_Reaction10+rate_Reaction11-rate_Reaction13+rate_Reaction14+rate_Reaction18+rate_Reaction9;
        result[12] = +rate_Reaction10-rate_Reaction11-rate_Reaction12;
        result[13] = +rate_Reaction13-rate_Reaction14-rate_Reaction15;
        result[14] = +rate_Reaction15-rate_Reaction16+rate_Reaction17-rate_Reaction19+rate_Reaction20+rate_Reaction21-rate_Reaction25+rate_Reaction26+rate_Reaction27;
        result[15] = +rate_Reaction16-rate_Reaction17-rate_Reaction18;
        result[16] = -rate_Reaction1+rate_Reaction2+rate_Reaction6;
        result[17] = -rate_Reaction1+rate_Reaction2+rate_Reaction3;
        result[18] = -rate_Reaction4+rate_Reaction5+rate_Reaction6;
        result[19] = +rate_Reaction1-rate_Reaction2-rate_Reaction3;
        result[20] = -rate_Reaction13+rate_Reaction14+rate_Reaction15+rate_Reaction3-rate_Reaction4+rate_Reaction5-rate_Reaction7+rate_Reaction8+rate_Reaction9;
        result[21] = +rate_Reaction4-rate_Reaction5-rate_Reaction6;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[22];
        __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 ...