/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000143.xml diagram  at 2008.03.20 15:09:21
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000143 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 = phagosome*(k1*x[10]*x[19] - kminus1*x[18]);
        rate_R10 = cytoplasm*k10*(x[3]/cytoplasm)*(x[5]/cytoplasm);
        rate_R11 = cytoplasm*k11*Math.pow((x[6]/cytoplasm), 2);
        rate_R12 = cytoplasm*k12;
        rate_R13a = cytoplasm*k13;
        rate_R13b = cytoplasm*kminus13*(x[8]/cytoplasm);
        rate_R14 = phagosome*(k14*x[14] - k14*(x[8]/cytoplasm));
        rate_R15 = phagosome*(k15*x[10] - k15*(x[0]/cytoplasm));
        rate_R16 = phagosome*(k16*x[12] - k16*(x[2]/cytoplasm));
        rate_R17 = phagosome*(k17*x[13] - k17*(x[3]/cytoplasm));
        rate_R18 = phagosome*(k18*x[15] - k18*(x[9]/cytoplasm));
        rate_R19 = phagosome*(V*(x[5]/cytoplasm)/Knadph*(1 + x[5]/cytoplasm/Knadph)*x[14]/((L + Math.pow((1 + x[5]/cytoplasm/Knadph), 2))*(Ko + x[14])));
        rate_R2 = phagosome*k2*x[18]*x[12];
        rate_R3 = phagosome*k3*x[17]*x[12];
        rate_R4 = phagosome*k4*x[19]*x[15];
        rate_R5 = phagosome*k5*Math.pow(x[15], 2);
        rate_R6 = phagosome*k6*x[16]*x[15];
        rate_R7 = cytoplasm*k7*(x[5]/cytoplasm)*(x[8]/cytoplasm);
        rate_R8 = cytoplasm*k8*(x[6]/cytoplasm)*(x[8]/cytoplasm);
        rate_R9 = cytoplasm*k9*Math.pow((x[9]/cytoplasm), 2);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        cytoplasm = 10.0; // initial value of $cytoplasm
        phagosome = 1.0; // initial value of $phagosome
        Knadph = 60.0; // initial value of Knadph
        Ko = 1.5; // initial value of Ko
        L = 550.0; // initial value of L
        V = 288.0; // initial value of V
        k1 = 50.0; // initial value of k1
        k10 = 10.0; // initial value of k10
        k11 = 60.0; // initial value of k11
        k12 = 25.0; // initial value of k12
        k13 = 12.5; // initial value of k13
        k14 = 30.0; // initial value of k14
        k15 = 30.0; // initial value of k15
        k16 = 10.0; // initial value of k16
        k17 = 10.0; // initial value of k17
        k18 = 2.0; // initial value of k18
        k2 = 10.0; // initial value of k2
        k3 = 0.0040; // initial value of k3
        k4 = 20.0; // initial value of k4
        k5 = 10.0; // initial value of k5
        k6 = 0.1; // initial value of k6
        k7 = 1.0E-6; // initial value of k7
        k8 = 50.0; // initial value of k8
        k9 = 500.0; // initial value of k9
        kminus1 = 58.0; // initial value of kminus1
        kminus13 = 0.045; // initial value of kminus13
    }

    /*
     * Model variables initial values
     */
    protected double rate_R1;
    protected double rate_R10;
    protected double rate_R11;
    protected double rate_R12;
    protected double rate_R13a;
    protected double rate_R13b;
    protected double rate_R14;
    protected double rate_R15;
    protected double rate_R16;
    protected double rate_R17;
    protected double rate_R18;
    protected double rate_R19;
    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 cytoplasm;
    protected double phagosome;
    protected double Knadph;
    protected double Ko;
    protected double L;
    protected double V;
    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 k2;
    protected double k3;
    protected double k4;
    protected double k5;
    protected double k6;
    protected double k7;
    protected double k8;
    protected double k9;
    protected double kminus1;
    protected double kminus13;

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


        double[] y = new double[20];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[20];
        this.time = 0.0;
        x[0] = 0.0; // - $"cytoplasm.H2O2_c"
        x[1] = 0.0; // - $"cytoplasm.H_c"
        x[2] = 3000.0; // - $"cytoplasm.MLTH_c"
        x[3] = 0.0; // - $"cytoplasm.MLT_c"
        x[4] = 0.0; // - $"cytoplasm.NADP2_c"
        x[5] = 0.0; // - $"cytoplasm.NADPH_c"
        x[6] = 0.0; // - $"cytoplasm.NADP_c"
        x[7] = 0.0; // - $"cytoplasm.NADPplus_c"
        x[8] = 0.0; // - $"cytoplasm.O2_c"
        x[9] = 0.0; // - $"cytoplasm.O2minus_c"
        x[10] = 0.0; // - $"phagosome.H2O2_p"
        x[11] = 0.0; // - $"phagosome.H_p"
        x[12] = 300.0; // - $"phagosome.MLTH_p"
        x[13] = 0.0; // - $"phagosome.MLT_p"
        x[14] = 0.0; // - $"phagosome.O2_p"
        x[15] = 0.0; // - $"phagosome.O2minus_p"
        x[16] = 0.0; // - $"phagosome.coIII_p"
        x[17] = 0.0; // - $"phagosome.coII_p"
        x[18] = 0.0; // - $"phagosome.coI_p"
        x[19] = 300.0; // - $"phagosome.per3_p"

        __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 'BIOMD0000000143.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_R15+rate_R7+rate_R9;
        result[1] = -rate_R9*2;
        result[2] = +rate_R10+rate_R16;
        result[3] = -rate_R10+rate_R17;
        result[4] = +rate_R11;
        result[5] = -rate_R10+rate_R12-rate_R19-rate_R7;
        result[6] = +rate_R10-rate_R11*2-rate_R8;
        result[7] = +rate_R19+rate_R7+rate_R8;
        result[8] = +rate_R13a-rate_R13b+rate_R14-rate_R7-rate_R8+rate_R9;
        result[9] = +rate_R18+rate_R8-rate_R9*2;
        result[10] = -rate_R15-rate_R1+rate_R5;
        result[11] = -rate_R5*2;
        result[12] = -rate_R16-rate_R2-rate_R3;
        result[13] = -rate_R17+rate_R2+rate_R3;
        result[14] = -rate_R14-rate_R19*2+rate_R5+rate_R6;
        result[15] = -rate_R18+rate_R19*2-rate_R4-rate_R5*2-rate_R6;
        result[16] = +rate_R4-rate_R6;
        result[17] = +rate_R2-rate_R3;
        result[18] = +rate_R1-rate_R2+rate_R6;
        result[19] = -rate_R1+rate_R3-rate_R4;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[20];
        __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 ...