/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000103.xml diagram  at 2008.03.20 15:08:39
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000103 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*(k1*x[0]*x[16] - kb1*x[1]);
        rate_v10 = cytosol*(k10*x[1]*x[14] - k10b*x[2]);
        rate_v11 = cytosol*(k11*x[11]*x[14] - k11b*x[12]);
        rate_v12 = cytosol*(k12*x[4]*x[14] - k12b*x[5]);
        rate_v13 = cytosol*(k13*x[9]*x[0] - k13b*x[2]);
        rate_v14 = cytosol*(k14*x[12]*x[0] - k14b*x[5]);
        rate_v15 = cytosol*(k15*x[7]*x[14] - k15b*x[8]);
        rate_v16 = cytosol*(k16prod - k16*x[0]);
        rate_v17 = cytosol*(k17prod - k17*x[16]);
        rate_v18 = cytosol*(k18prod - k18*x[14]);
        rate_v19 = cytosol*k19*x[9];
        rate_v2 = cytosol*k2*x[15]*x[16];
        rate_v20 = cytosol*k20*x[2];
        rate_v21 = cytosol*k21*x[1];
        rate_v22 = cytosol*(k22prod - k22*x[15]);
        rate_v23 = cytosol*k23*x[7];
        rate_v24 = cytosol*k24*x[8];
        rate_v25 = cytosol*k25*x[12];
        rate_v26 = cytosol*k26*x[11];
        rate_v27 = cytosol*k27*x[4];
        rate_v28 = cytosol*k28*x[5];
        rate_v29 = cytosol*k29*x[10];
        rate_v3 = cytosol*k3*x[15]*x[1];
        rate_v30 = cytosol*k30*x[6];
        rate_v31 = cytosol*k31*x[13];
        rate_v32 = cytosol*k32*x[6];
        rate_v33 = cytosol*(a*k15*x[7]*x[9] - d*k15b*x[10]);
        rate_v34 = cytosol*(a*k15*x[7]*x[2] - d*k15b*x[3]);
        rate_v35 = cytosol*(a*k15*x[7]*x[12] - d*k15b*x[13]);
        rate_v36 = cytosol*(a*k15*x[7]*x[5] - d*k15b*x[6]);
        rate_v37 = cytosol*(a*k9*x[16]*x[8] - d*k9b*x[10]);
        rate_v38 = cytosol*(a*k9*x[1]*x[8] - d*k9b*x[3]);
        rate_v39 = cytosol*(a*k9*x[11]*x[8] - d*k9b*x[13]);
        rate_v4 = cytosol*k4*x[16]*x[7];
        rate_v40 = cytosol*(a*k9*x[4]*x[8] - d*k9b*x[6]);
        rate_v41 = cytosol*(a*k1*x[10]*x[0] - d*kb1*x[3]);
        rate_v42 = cytosol*(a*k1*x[13]*x[0] - d*kb1*x[6]);
        rate_v5 = cytosol*k5*x[1]*x[7];
        rate_v6 = cytosol*k6*x[15]*x[11];
        rate_v7 = cytosol*k7*x[15]*x[4];
    }
    public void __internalRateVarInitFunc_1(double time, double[] x)
    {
        rate_v8 = cytosol*(k8*x[11]*x[0] - k8b*x[4]);
        rate_v9 = cytosol*(k9*x[16]*x[14] - k9b*x[9]);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        cytosol = 1.0; // initial value of $cytosol
        a = 1.0; // initial value of a
        d = 1.0; // initial value of d
        k1 = 0.0020; // initial value of k1
        k10 = 0.0010; // initial value of k10
        k10b = 0.0010; // initial value of k10b
        k11 = 0.0010; // initial value of k11
        k11b = 0.0010; // initial value of k11b
        k12 = 0.0010; // initial value of k12
        k12b = 0.0010; // initial value of k12b
        k13 = 0.0020; // initial value of k13
        k13b = 0.1; // initial value of k13b
        k14 = 0.0020; // initial value of k14
        k14b = 0.1; // initial value of k14b
        k15 = 0.0030; // initial value of k15
        k15b = 0.0010; // initial value of k15b
        k16 = 0.0010; // initial value of k16
        k16prod = 0.02; // initial value of k16prod
        k17 = 0.0010; // initial value of k17
        k17prod = 0.02; // initial value of k17prod
        k18 = 0.0010; // initial value of k18
        k18prod = 0.04; // initial value of k18prod
        k19 = 0.0010; // initial value of k19
        k2 = 5.0E-6; // initial value of k2
        k20 = 0.0010; // initial value of k20
        k21 = 0.0010; // initial value of k21
        k22 = 0.0010; // initial value of k22
        k22prod = 0.2; // initial value of k22prod
        k23 = 0.0010; // initial value of k23
        k24 = 0.0010; // initial value of k24
        k25 = 0.0010; // initial value of k25
        k26 = 0.0010; // initial value of k26
        k27 = 0.0010; // initial value of k27
        k28 = 0.0010; // initial value of k28
        k29 = 0.0010; // initial value of k29
        k3 = 3.5E-4; // initial value of k3
        k30 = 0.0010; // initial value of k30
        k31 = 0.0010; // initial value of k31
        k32 = 0.0010; // initial value of k32
        k4 = 2.0E-4; // initial value of k4
        k5 = 2.0E-4; // initial value of k5
        k6 = 5.0E-5; // initial value of k6
        k7 = 0.0035; // initial value of k7
        k8 = 0.0020; // initial value of k8
        k8b = 0.1; // initial value of k8b
        k9 = 0.0010; // initial value of k9
        k9b = 0.0010; // initial value of k9b
        kb1 = 0.1; // initial value of kb1
    }

    /*
     * Model variables initial values
     */
    protected double rate_v1;
    protected double rate_v10;
    protected double rate_v11;
    protected double rate_v12;
    protected double rate_v13;
    protected double rate_v14;
    protected double rate_v15;
    protected double rate_v16;
    protected double rate_v17;
    protected double rate_v18;
    protected double rate_v19;
    protected double rate_v2;
    protected double rate_v20;
    protected double rate_v21;
    protected double rate_v22;
    protected double rate_v23;
    protected double rate_v24;
    protected double rate_v25;
    protected double rate_v26;
    protected double rate_v27;
    protected double rate_v28;
    protected double rate_v29;
    protected double rate_v3;
    protected double rate_v30;
    protected double rate_v31;
    protected double rate_v32;
    protected double rate_v33;
    protected double rate_v34;
    protected double rate_v35;
    protected double rate_v36;
    protected double rate_v37;
    protected double rate_v38;
    protected double rate_v39;
    protected double rate_v4;
    protected double rate_v40;
    protected double rate_v41;
    protected double rate_v42;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double cytosol;
    protected double a;
    protected double d;
    protected double k1;
    protected double k10;
    protected double k10b;
    protected double k11;
    protected double k11b;
    protected double k12;
    protected double k12b;
    protected double k13;
    protected double k13b;
    protected double k14;
    protected double k14b;
    protected double k15;
    protected double k15b;
    protected double k16;
    protected double k16prod;
    protected double k17;
    protected double k17prod;
    protected double k18;
    protected double k18prod;
    protected double k19;
    protected double k2;
    protected double k20;
    protected double k21;
    protected double k22;
    protected double k22prod;
    protected double k23;
    protected double k24;
    protected double k25;
    protected double k26;
    protected double k27;
    protected double k28;
    protected double k29;
    protected double k3;
    protected double k30;
    protected double k31;
    protected double k32;
    protected double k4;
    protected double k5;
    protected double k6;
    protected double k7;
    protected double k8;
    protected double k8b;
    protected double k9;
    protected double k9b;
    protected double kb1;

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


        double[] y = new double[17];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[17];
        this.time = 0.0;
        x[0] = 20.0; // - $"cytosol.A"
        x[1] = 0.0; // - $"cytosol.AC9"
        x[2] = 0.0; // - $"cytosol.AC9X"
        x[3] = 0.0; // - $"cytosol.AC9X_C3_star"
        x[4] = 0.0; // - $"cytosol.AC9_star"
        x[5] = 0.0; // - $"cytosol.AC9_starX"
        x[6] = 0.0; // - $"cytosol.AC9_starX_C3_star"
        x[7] = 0.0; // - $"cytosol.C3_star"
        x[8] = 0.0; // - $"cytosol.C3_starX"
        x[9] = 0.0; // - $"cytosol.C9X"
        x[10] = 0.0; // - $"cytosol.C9X_C3_star"
        x[11] = 0.0; // - $"cytosol.C9_star"
        x[12] = 0.0; // - $"cytosol.C9_starX"
        x[13] = 0.0; // - $"cytosol.C9_starX_C3_star"
        x[14] = 40.0; // - $"cytosol.X"
        x[15] = 200.0; // - $cytosol.C3
        x[16] = 20.0; // - $cytosol.C9

        __internalRateVarInitFunc_0(time, x);
        __internalRateVarInitFunc_1(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);
        __internalRateVarInitFunc_1(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000103.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v13-rate_v14+rate_v16-rate_v1-rate_v41-rate_v42-rate_v8;
        result[1] = -rate_v10+rate_v1-rate_v21-rate_v38+rate_v3-rate_v3-rate_v5;
        result[2] = +rate_v10+rate_v13-rate_v20-rate_v34;
        result[3] = +rate_v34+rate_v38+rate_v41;
        result[4] = -rate_v12-rate_v27-rate_v40+rate_v5+rate_v7-rate_v7+rate_v8;
        result[5] = +rate_v12+rate_v14-rate_v28-rate_v36;
        result[6] = -rate_v30-rate_v32+rate_v36+rate_v40+rate_v42;
        result[7] = -rate_v15-rate_v23+rate_v2-rate_v33-rate_v34-rate_v35-rate_v36+rate_v3+rate_v4-rate_v4+rate_v5-rate_v5+rate_v6+rate_v7;
        result[8] = +rate_v15-rate_v24-rate_v37-rate_v38-rate_v39-rate_v40;
        result[9] = -rate_v13-rate_v19-rate_v33+rate_v9;
        result[10] = -rate_v29+rate_v33+rate_v37-rate_v41;
        result[11] = -rate_v11-rate_v26-rate_v39+rate_v4+rate_v6-rate_v6-rate_v8;
        result[12] = +rate_v11-rate_v14-rate_v25-rate_v35;
        result[13] = -rate_v31+rate_v35+rate_v39-rate_v42;
        result[14] = -rate_v10-rate_v11-rate_v12-rate_v15+rate_v18-rate_v9;
        result[15] = +rate_v22-rate_v2-rate_v3-rate_v6-rate_v7;
        result[16] = +rate_v17-rate_v1+rate_v2-rate_v2-rate_v37-rate_v4-rate_v9;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[17];
        __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 ...