/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000048.xml diagram  at 2008.03.20 15:04:27
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000048 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 = (v1_k1f*(x[5]/compartment)*(x[0]/compartment) - v1_k1b*(x[22]/compartment))*compartment;
        rate_v10 = (v10_k10f*(x[20]/compartment)*(x[13]/compartment) - v10_k10b*(x[6]/compartment))*compartment;
        rate_v11 = (v11_k11f*(x[6]/compartment) - v11_k11b*(x[21]/compartment)*(x[18]/compartment))*compartment;
        rate_v12 = (v12_k12f*(x[18]/compartment) - v12_k12b*(x[1]/compartment)*(x[13]/compartment))*compartment;
        rate_v13 = (v13_k13f*(x[21]/compartment)*(x[17]/compartment) - v13_k13b*(x[9]/compartment))*compartment;
        rate_v14 = (v14_k14f*(x[9]/compartment) - v14_k14b*(x[12]/compartment))*compartment;
        rate_v15 = (v15_k15f*(x[12]/compartment) - v15_k15b*(x[16]/compartment)*(x[21]/compartment))*compartment;
        rate_v16 = v16_V16*(x[16]/compartment)/(v16_K16 + x[16]/compartment)*compartment;
        rate_v17 = (v17_k17f*(x[12]/compartment)*(x[1]/compartment) - v17_k17b*(x[10]/compartment))*compartment;
        rate_v18 = (v18_k18f*(x[10]/compartment) - v18_k18b*(x[21]/compartment)*(x[14]/compartment))*compartment;
        rate_v19 = (v19_k19f*(x[10]/compartment)*(x[13]/compartment) - v19_k19b*(x[11]/compartment))*compartment;
        rate_v2 = (v2_k2f*(x[22]/compartment)*(x[22]/compartment) - v2_k2b*(x[19]/compartment))*compartment;
        rate_v20 = (v20_k20f*(x[11]/compartment) - v20_k20b*(x[15]/compartment)*(x[21]/compartment))*compartment;
        rate_v21 = (v21_k21f*(x[16]/compartment)*(x[1]/compartment) - v21_k21b*(x[14]/compartment))*compartment;
        rate_v22 = (v22_k22f*(x[14]/compartment)*(x[13]/compartment) - v22_k22b*(x[15]/compartment))*compartment;
        rate_v23 = (v23_k23f*(x[15]/compartment) - v23_k23b*(x[16]/compartment)*(x[18]/compartment))*compartment;
        rate_v24 = (v24_k24f*(x[12]/compartment)*(x[18]/compartment) - v24_k24b*(x[11]/compartment))*compartment;
        rate_v25 = (v25_k25f*(x[3]/compartment) - v25_k25b*(x[4]/compartment))*compartment;
        rate_v3 = (v3_k3f*(x[19]/compartment) - v3_k3b*(x[21]/compartment))*compartment;
        rate_v4 = v4_V4*(x[21]/compartment)/(v4_K4 + x[21]/compartment)*compartment;
        rate_v5 = (v5_k5f*(x[21]/compartment)*(x[2]/compartment) - v5_k5b*(x[7]/compartment))*compartment;
        rate_v6 = (v6_k6f*(x[7]/compartment) - v6_k6b*(x[8]/compartment))*compartment;
        rate_v7 = (v7_k7f*(x[8]/compartment) - v7_k7b*(x[21]/compartment)*(x[3]/compartment))*compartment;
        rate_v8 = v8_V8*(x[3]/compartment)/(v8_K8 + x[3]/compartment)*compartment;
        rate_v9 = (v9_k9f*(x[21]/compartment)*(x[1]/compartment) - v9_k9b*(x[20]/compartment))*compartment;
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        compartment = 3.0E-12; // initial value of $compartment
        v10_k10b = 0.06; // initial value of v10_k10b
        v10_k10f = 0.01; // initial value of v10_k10f
        v11_k11b = 0.0045; // initial value of v11_k11b
        v11_k11f = 0.03; // initial value of v11_k11f
        v12_k12b = 1.0E-4; // initial value of v12_k12b
        v12_k12f = 0.0015; // initial value of v12_k12f
        v13_k13b = 0.6; // initial value of v13_k13b
        v13_k13f = 0.09; // initial value of v13_k13f
        v14_k14b = 0.06; // initial value of v14_k14b
        v14_k14f = 6.0; // initial value of v14_k14f
        v15_k15b = 9.0E-4; // initial value of v15_k15b
        v15_k15f = 0.3; // initial value of v15_k15f
        v16_K16 = 340.0; // initial value of v16_K16
        v16_V16 = 1.7; // initial value of v16_V16
        v17_k17b = 0.1; // initial value of v17_k17b
        v17_k17f = 0.0030; // initial value of v17_k17f
        v18_k18b = 9.0E-4; // initial value of v18_k18b
        v18_k18f = 0.3; // initial value of v18_k18f
        v19_k19b = 0.0214; // initial value of v19_k19b
        v19_k19f = 0.01; // initial value of v19_k19f
        v1_k1b = 0.06; // initial value of v1_k1b
        v1_k1f = 0.0030; // initial value of v1_k1f
        v20_k20b = 2.4E-4; // initial value of v20_k20b
        v20_k20f = 0.12; // initial value of v20_k20f
        v21_k21b = 0.1; // initial value of v21_k21b
        v21_k21f = 0.0030; // initial value of v21_k21f
        v22_k22b = 0.064; // initial value of v22_k22b
        v22_k22f = 0.03; // initial value of v22_k22f
        v23_k23b = 0.021; // initial value of v23_k23b
        v23_k23f = 0.1; // initial value of v23_k23f
        v24_k24b = 0.0429; // initial value of v24_k24b
        v24_k24f = 0.0090; // initial value of v24_k24f
        v25_k25b = 0.03; // initial value of v25_k25b
        v25_k25f = 1.0; // initial value of v25_k25f
        v2_k2b = 0.1; // initial value of v2_k2b
        v2_k2f = 0.01; // initial value of v2_k2f
        v3_k3b = 0.01; // initial value of v3_k3b
        v3_k3f = 1.0; // initial value of v3_k3f
        v4_K4 = 50.0; // initial value of v4_K4
        v4_V4 = 450.0; // initial value of v4_V4
        v5_k5b = 0.2; // initial value of v5_k5b
        v5_k5f = 0.06; // initial value of v5_k5f
        v6_k6b = 0.05; // initial value of v6_k6b
        v6_k6f = 1.0; // initial value of v6_k6f
        v7_k7b = 0.0060; // initial value of v7_k7b
        v7_k7f = 0.3; // initial value of v7_k7f
        v8_K8 = 100.0; // initial value of v8_K8
        v8_V8 = 1.0; // initial value of v8_V8
        v9_k9b = 0.05; // initial value of v9_k9b
        v9_k9f = 0.0030; // initial value of v9_k9f
    }

    /*
     * 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_v3;
    protected double rate_v4;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double compartment;
    protected double v10_k10b;
    protected double v10_k10f;
    protected double v11_k11b;
    protected double v11_k11f;
    protected double v12_k12b;
    protected double v12_k12f;
    protected double v13_k13b;
    protected double v13_k13f;
    protected double v14_k14b;
    protected double v14_k14f;
    protected double v15_k15b;
    protected double v15_k15f;
    protected double v16_K16;
    protected double v16_V16;
    protected double v17_k17b;
    protected double v17_k17f;
    protected double v18_k18b;
    protected double v18_k18f;
    protected double v19_k19b;
    protected double v19_k19f;
    protected double v1_k1b;
    protected double v1_k1f;
    protected double v20_k20b;
    protected double v20_k20f;
    protected double v21_k21b;
    protected double v21_k21f;
    protected double v22_k22b;
    protected double v22_k22f;
    protected double v23_k23b;
    protected double v23_k23f;
    protected double v24_k24b;
    protected double v24_k24f;
    protected double v25_k25b;
    protected double v25_k25f;
    protected double v2_k2b;
    protected double v2_k2f;
    protected double v3_k3b;
    protected double v3_k3f;
    protected double v4_K4;
    protected double v4_V4;
    protected double v5_k5b;
    protected double v5_k5f;
    protected double v6_k6b;
    protected double v6_k6f;
    protected double v7_k7b;
    protected double v7_k7f;
    protected double v8_K8;
    protected double v8_V8;
    protected double v9_k9b;
    protected double v9_k9f;

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


        double[] y = new double[23];
        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];
        y[22] = x[22];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[23];
        this.time = 0.0;
        x[0] = 2.04E-9; // - $"compartment.EGF"
        x[1] = 2.55E-10; // - $"compartment.Grb"
        x[2] = 3.15E-10; // - $"compartment.PLCg"
        x[3] = 0.0; // - $"compartment.PLCgP"
        x[4] = 0.0; // - $"compartment.PLCgl"
        x[5] = 3.0E-10; // - $"compartment.R"
        x[6] = 0.0; // - $"compartment.RGS"
        x[7] = 0.0; // - $"compartment.RPLCg"
        x[8] = 0.0; // - $"compartment.RPLCgP"
        x[9] = 0.0; // - $"compartment.RSh"
        x[10] = 0.0; // - $"compartment.RShG"
        x[11] = 0.0; // - $"compartment.RShGS"
        x[12] = 0.0; // - $"compartment.RShP"
        x[13] = 1.0200000000000001E-10; // - $"compartment.SOS"
        x[14] = 0.0; // - $"compartment.ShG"
        x[15] = 0.0; // - $"compartment.ShGS"
        x[16] = 0.0; // - $"compartment.ShP"
        x[17] = 4.5E-10; // - $"compartment.Shc"
        x[18] = 0.0; // - $compartment.GS
        x[19] = 0.0; // - $compartment.R2
        x[20] = 0.0; // - $compartment.RG
        x[21] = 0.0; // - $compartment.RP
        x[22] = 0.0; // - $compartment.Ra

        __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 'BIOMD0000000048.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v1;
        result[1] = +rate_v12-rate_v17-rate_v21-rate_v9;
        result[2] = -rate_v5+rate_v8;
        result[3] = -rate_v25+rate_v7-rate_v8;
        result[4] = +rate_v25;
        result[5] = -rate_v1;
        result[6] = +rate_v10-rate_v11;
        result[7] = +rate_v5-rate_v6;
        result[8] = +rate_v6-rate_v7;
        result[9] = +rate_v13-rate_v14;
        result[10] = +rate_v17-rate_v18-rate_v19;
        result[11] = +rate_v19-rate_v20+rate_v24;
        result[12] = +rate_v14-rate_v15-rate_v17-rate_v24;
        result[13] = -rate_v10+rate_v12-rate_v19-rate_v22;
        result[14] = +rate_v18+rate_v21-rate_v22;
        result[15] = +rate_v20+rate_v22-rate_v23;
        result[16] = +rate_v15-rate_v16-rate_v21+rate_v23;
        result[17] = -rate_v13+rate_v16;
        result[18] = +rate_v11-rate_v12+rate_v23-rate_v24;
        result[19] = +rate_v2-rate_v3+rate_v4;
        result[20] = -rate_v10+rate_v9;
        result[21] = +rate_v11-rate_v13+rate_v15+rate_v18+rate_v20+rate_v3-rate_v4-rate_v5+rate_v7-rate_v9;
        result[22] = +rate_v1-rate_v2*2;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[23];
        __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 ...