/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000017.xml diagram  at 2008.03.20 15:03:55
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000017 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 = R1_V_1*(_compartment_halfglucose_/R1_Kglc_1)*(x[9]/R1_Knad_1)*(x[0]/R1_Kadp_1)/((1 + _compartment_halfglucose_/R1_Kglc_1 + x[11]/R1_Kpyr_1)*(1 + x[9]/R1_Knad_1 + x[10]/R1_Knadh_1)*(1 + x[0]/R1_Kadp_1 + x[1]/R1_Katp_1));
        rate_R10 = R10_V_10*(x[6]/R10_Kacet_10)/(1 + x[6]/R10_Kacet_10);
        rate_R11 = R11_V_11*((x[6]*x[10] - _compartment_Butanediol_*x[9]/R11_Keq_11)/(R11_Kacet_11*R11_Knadh_11))/((1 + x[6]/R11_Kacet_11 + _compartment_Butanediol_/R11_Kbut_11)*(1 + x[10]/R11_Knadh_11 + x[9]/R11_Knad_11));
        rate_R12 = R12_V_12*Math.pow((x[1]/(x[0]*R12_Katp_12)), R12_n_12)/(1 + Math.pow((x[1]/(x[0]*R12_Katp_12)), R12_n_12));
        rate_R13 = R13_V_13*(x[10]*compartment_O2/(R13_Knadh_13*R13_Ko_13))/((1 + x[10]/R13_Knadh_13 + x[9]/R13_Knad_13)*(1 + compartment_O2/R13_Ko_13));
        rate_R14 = R14_k_14*x[3];
        rate_R2 = R2_V_2*((x[11]*x[10] - _compartment_lactate_*x[9]/R2_Keq_2)/(R2_Kpyr_2*R2_Knadh_2))/((1 + x[11]/R2_Kpyr_2 + _compartment_lactate_/R2_Klac_2)*(1 + x[10]/R2_Knadh_2 + x[9]/R2_Knad_2));
        rate_R3 = R3_V_3*(x[11]/R3_Kpyr_3)*(x[9]/R3_Knad_3)*(x[8]/R3_Kcoa_3)*(x[9]/(x[9] + R3_Ki_3*x[10]))/((1 + x[11]/R3_Kpyr_3)*(1 + x[9]/R3_Knad_3 + x[10]/R3_Knadh_3)*(1 + x[8]/R3_Kcoa_3 + x[2]/R3_Kaccoa_3));
        rate_R4 = R4_V_4*((x[2]*_compartment_PO4_ - x[5]*x[8]/R4_Keq_4)/(R4_Kiaccoa_4*R4_Kpi_4))/(1 + x[2]/R4_Kiaccoa_4 + _compartment_PO4_/R4_Kipi_4 + x[5]/R4_Kiacp_4 + x[8]/R4_Kicoa_4 + x[2]*_compartment_PO4_/(R4_Kiaccoa_4*R4_Kpi_4) + x[5]*x[8]/(R4_Kacp_4*R4_Kicoa_4));
        rate_R5 = R5_V_5*((x[5]*x[0] - compartment_Ac*x[1]/R5_Keq_5)/(R5_Kadp_5*R5_Kacp_5))/((1 + x[5]/R5_Kacp_5 + compartment_Ac/R5_Kac_5)*(1 + x[0]/R5_Kadp_5 + x[1]/R5_Katp_5));
        rate_R6 = R6_V_6*((x[2]*x[10] - x[8]*x[9]*x[4]/R6_Keq_6)/(R6_Kaccoa_6*R6_Knadh_6))/((1 + x[9]/R6_Knad_6 + x[10]/R6_Knadh_6)*(1 + x[2]/R6_Kaccoa_6 + x[8]/R6_Kcoa_6 + x[4]/R6_Kaco_6 + x[4]*x[8]/(R6_Kaco_6*R6_Kcoa_6)));
        rate_R7 = R7_V_7*((x[4]*x[10] - _compartment_EtOH_*x[9]/R7_Keq_7)/(R7_Kaco_7*R7_Knadh_7))/((1 + x[9]/R7_Knad_7 + x[10]/R7_Knadh_7)*(1 + x[4]/R7_Kaco_7 + _compartment_EtOH_/R7_Ketoh_7));
        rate_R8 = R8_V_8*(x[11]/R8_Kpyr_8)*(1 - x[3]/(x[11]*R8_Keq_8))*Math.pow((x[11]/R8_Kpyr_8 + x[3]/R8_Kaclac_8), (R8_n_8 - 1))/(1 + Math.pow((x[11]/R8_Kpyr_8 + x[3]/R8_Kaclac_8), R8_n_8));
        rate_R9 = R9_V_9*(x[3]/R9_Kaclac_9)/(1 + x[3]/R9_Kaclac_9 + x[6]/R9_Kacet_9);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _compartment_Butanediol_ = 0.01; // initial value of $"compartment.Butanediol"
        _compartment_EtOH_ = 1.0; // initial value of $"compartment.EtOH"
        _compartment_PO4_ = 10.0; // initial value of $"compartment.PO4"
        _compartment_halfglucose_ = 30.0; // initial value of $"compartment.halfglucose"
        _compartment_lactate_ = 1.0; // initial value of $"compartment.lactate"
        compartment_Ac = 1.0; // initial value of $compartment.Ac
        compartment_O2 = 0.2; // initial value of $compartment.O2
        R10_Kacet_10 = 5.0; // initial value of R10_Kacet_10
        R10_V_10 = 200.0; // initial value of R10_V_10
        R11_Kacet_11 = 0.06; // initial value of R11_Kacet_11
        R11_Kbut_11 = 2.6; // initial value of R11_Kbut_11
        R11_Keq_11 = 1400.0; // initial value of R11_Keq_11
        R11_Knad_11 = 0.16; // initial value of R11_Knad_11
        R11_Knadh_11 = 0.02; // initial value of R11_Knadh_11
        R11_V_11 = 105.0; // initial value of R11_V_11
        R12_Katp_12 = 6.2; // initial value of R12_Katp_12
        R12_V_12 = 900.0; // initial value of R12_V_12
        R12_n_12 = 2.6; // initial value of R12_n_12
        R13_Knad_13 = 1.0; // initial value of R13_Knad_13
        R13_Knadh_13 = 0.041; // initial value of R13_Knadh_13
        R13_Ko_13 = 0.01; // initial value of R13_Ko_13
        R13_V_13 = 118.0; // initial value of R13_V_13
        R14_k_14 = 3.0E-4; // initial value of R14_k_14
        R1_Kadp_1 = 0.047; // initial value of R1_Kadp_1
        R1_Katp_1 = 0.019; // initial value of R1_Katp_1
        R1_Kglc_1 = 0.1; // initial value of R1_Kglc_1
        R1_Knad_1 = 0.14; // initial value of R1_Knad_1
        R1_Knadh_1 = 0.09; // initial value of R1_Knadh_1
        R1_Kpyr_1 = 25.0; // initial value of R1_Kpyr_1
        R1_V_1 = 2397.0; // initial value of R1_V_1
        R2_Keq_2 = 21120.7; // initial value of R2_Keq_2
        R2_Klac_2 = 100.0; // initial value of R2_Klac_2
        R2_Knad_2 = 2.4; // initial value of R2_Knad_2
        R2_Knadh_2 = 0.08; // initial value of R2_Knadh_2
        R2_Kpyr_2 = 1.5; // initial value of R2_Kpyr_2
        R2_V_2 = 5118.0; // initial value of R2_V_2
        R3_Kaccoa_3 = 0.0080; // initial value of R3_Kaccoa_3
        R3_Kcoa_3 = 0.014; // initial value of R3_Kcoa_3
        R3_Ki_3 = 46.4; // initial value of R3_Ki_3
        R3_Knad_3 = 0.4; // initial value of R3_Knad_3
        R3_Knadh_3 = 0.1; // initial value of R3_Knadh_3
        R3_Kpyr_3 = 1.0; // initial value of R3_Kpyr_3
        R3_V_3 = 259.0; // initial value of R3_V_3
        R4_Kacp_4 = 0.7; // initial value of R4_Kacp_4
        R4_Keq_4 = 0.0281; // initial value of R4_Keq_4
        R4_Kiaccoa_4 = 0.2; // initial value of R4_Kiaccoa_4
        R4_Kiacp_4 = 0.2; // initial value of R4_Kiacp_4
        R4_Kicoa_4 = 0.029; // initial value of R4_Kicoa_4
        R4_Kipi_4 = 2.6; // initial value of R4_Kipi_4
        R4_Kpi_4 = 2.6; // initial value of R4_Kpi_4
        R4_V_4 = 42.0; // initial value of R4_V_4
        R5_Kac_5 = 7.0; // initial value of R5_Kac_5
        R5_Kacp_5 = 0.16; // initial value of R5_Kacp_5
        R5_Kadp_5 = 0.5; // initial value of R5_Kadp_5
        R5_Katp_5 = 0.07; // initial value of R5_Katp_5
        R5_Keq_5 = 174.2; // initial value of R5_Keq_5
        R5_V_5 = 2700.0; // initial value of R5_V_5
        R6_Kaccoa_6 = 0.0070; // initial value of R6_Kaccoa_6
        R6_Kaco_6 = 10.0; // initial value of R6_Kaco_6
        R6_Kcoa_6 = 0.0080; // initial value of R6_Kcoa_6
        R6_Keq_6 = 1.0; // initial value of R6_Keq_6
        R6_Knad_6 = 0.08; // initial value of R6_Knad_6
        R6_Knadh_6 = 0.025; // initial value of R6_Knadh_6
        R6_V_6 = 97.0; // initial value of R6_V_6
        R7_Kaco_7 = 0.03; // initial value of R7_Kaco_7
        R7_Keq_7 = 12354.9; // initial value of R7_Keq_7
        R7_Ketoh_7 = 1.0; // initial value of R7_Ketoh_7
        R7_Knad_7 = 0.08; // initial value of R7_Knad_7
        R7_Knadh_7 = 0.05; // initial value of R7_Knadh_7
        R7_V_7 = 162.0; // initial value of R7_V_7
        R8_Kaclac_8 = 100.0; // initial value of R8_Kaclac_8
        R8_Keq_8 = 9.0E12; // initial value of R8_Keq_8
        R8_Kpyr_8 = 50.0; // initial value of R8_Kpyr_8
        R8_V_8 = 600.0; // initial value of R8_V_8
        R8_n_8 = 2.4; // initial value of R8_n_8
        R9_Kacet_9 = 100.0; // initial value of R9_Kacet_9
        R9_Kaclac_9 = 10.0; // initial value of R9_Kaclac_9
        R9_V_9 = 106.0; // initial value of R9_V_9
    }

    /*
     * Model variables initial values
     */
    protected double _compartment_Butanediol_;
    protected double _compartment_EtOH_;
    protected double _compartment_PO4_;
    protected double _compartment_halfglucose_;
    protected double _compartment_lactate_;
    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_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 compartment_Ac;
    protected double compartment_O2;
    protected double R10_Kacet_10;
    protected double R10_V_10;
    protected double R11_Kacet_11;
    protected double R11_Kbut_11;
    protected double R11_Keq_11;
    protected double R11_Knad_11;
    protected double R11_Knadh_11;
    protected double R11_V_11;
    protected double R12_Katp_12;
    protected double R12_V_12;
    protected double R12_n_12;
    protected double R13_Knad_13;
    protected double R13_Knadh_13;
    protected double R13_Ko_13;
    protected double R13_V_13;
    protected double R14_k_14;
    protected double R1_Kadp_1;
    protected double R1_Katp_1;
    protected double R1_Kglc_1;
    protected double R1_Knad_1;
    protected double R1_Knadh_1;
    protected double R1_Kpyr_1;
    protected double R1_V_1;
    protected double R2_Keq_2;
    protected double R2_Klac_2;
    protected double R2_Knad_2;
    protected double R2_Knadh_2;
    protected double R2_Kpyr_2;
    protected double R2_V_2;
    protected double R3_Kaccoa_3;
    protected double R3_Kcoa_3;
    protected double R3_Ki_3;
    protected double R3_Knad_3;
    protected double R3_Knadh_3;
    protected double R3_Kpyr_3;
    protected double R3_V_3;
    protected double R4_Kacp_4;
    protected double R4_Keq_4;
    protected double R4_Kiaccoa_4;
    protected double R4_Kiacp_4;
    protected double R4_Kicoa_4;
    protected double R4_Kipi_4;
    protected double R4_Kpi_4;
    protected double R4_V_4;
    protected double R5_Kac_5;
    protected double R5_Kacp_5;
    protected double R5_Kadp_5;
    protected double R5_Katp_5;
    protected double R5_Keq_5;
    protected double R5_V_5;
    protected double R6_Kaccoa_6;
    protected double R6_Kaco_6;
    protected double R6_Kcoa_6;
    protected double R6_Keq_6;
    protected double R6_Knad_6;
    protected double R6_Knadh_6;
    protected double R6_V_6;
    protected double R7_Kaco_7;
    protected double R7_Keq_7;
    protected double R7_Ketoh_7;
    protected double R7_Knad_7;
    protected double R7_Knadh_7;
    protected double R7_V_7;
    protected double R8_Kaclac_8;
    protected double R8_Keq_8;
    protected double R8_Kpyr_8;
    protected double R8_V_8;
    protected double R8_n_8;
    protected double R9_Kacet_9;
    protected double R9_Kaclac_9;
    protected double R9_V_9;

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


        double[] y = new double[12];
        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];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[12];
        this.time = 0.0;
        x[0] = 5.0; // - $"compartment.ADP"
        x[1] = 0.0; // - $"compartment.ATP"
        x[2] = 0.0; // - $"compartment.AcCoA"
        x[3] = 0.0; // - $"compartment.AcLac"
        x[4] = 0.0; // - $"compartment.AcO"
        x[5] = 0.0; // - $"compartment.AcP"
        x[6] = 0.0; // - $"compartment.AcetoinIn"
        x[7] = 0.0; // - $"compartment.AcetoinOut"
        x[8] = 1.0; // - $"compartment.CoA"
        x[9] = 10.0; // - $"compartment.NAD"
        x[10] = 0.0; // - $"compartment.NADH"
        x[11] = 1.0E-12; // - $"compartment.pyruvate"

        __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 'BIOMD0000000017.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_R12-rate_R1-rate_R5;
        result[1] = -rate_R12+rate_R1+rate_R5;
        result[2] = +rate_R3-rate_R4-rate_R6;
        result[3] = -rate_R14+rate_R8*2-rate_R9;
        result[4] = +rate_R6-rate_R7;
        result[5] = +rate_R4-rate_R5;
        result[6] = -rate_R10-rate_R11+rate_R14+rate_R9;
        result[7] = +rate_R10;
        result[8] = -rate_R3+rate_R4+rate_R6;
        result[9] = +rate_R11+rate_R13-rate_R1+rate_R2-rate_R3+rate_R6+rate_R7;
        result[10] = -rate_R11-rate_R13+rate_R1-rate_R2+rate_R3-rate_R6-rate_R7;
        result[11] = +rate_R1-rate_R2-rate_R3-rate_R8;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[12];
        __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 ...