/* * This code is generated by BioUML FrameWork * for BIOMD0000000108.xml diagram at 2008.03.20 15:08:44 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000108 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { HO2star = x[0]/100; Cu_I_ZnSOD = _compartment_0000001_species_0000016_ - x[1]; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_fast = k10*HO2star*compartment_0000001; rate_reaction_0 = compartment_0000001*k2*x[0]*x[1]; rate_reaction_0000001 = compartment_0000001*k1; rate_reaction_1 = compartment_0000001*k3*x[0]*Cu_I_ZnSOD; rate_reaction_10 = compartment_0000001*k13a*Cu_I_ZnSOD; rate_reaction_11 = compartment_0000001*k13b*x[1]; rate_reaction_12 = compartment_0000001*k17*x[6]; rate_reaction_13 = compartment_0000001*k18*x[3]; rate_reaction_14 = compartment_0000001*k19*Math.pow(x[3], 2.0); rate_reaction_2 = compartment_0000001*k4*x[0]*x[3]; rate_reaction_3 = compartment_0000001*k5*x[0]*x[2]; rate_reaction_4 = compartment_0000001*k6*x[2]*x[1]; rate_reaction_5 = compartment_0000001*k7*x[2]*_compartment_0000001_species_0000017_; rate_reaction_6 = compartment_0000001*k9*x[4]; rate_reaction_7 = compartment_0000001*k10*HO2star; rate_reaction_8 = compartment_0000001*k11*x[4]; rate_reaction_9 = compartment_0000001*k12*x[5]; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _compartment_0000001_species_0000016_ = 1.0E-5; // initial value of $"compartment_0000001.species_0000016" _compartment_0000001_species_0000017_ = 1.0E-5; // initial value of $"compartment_0000001.species_0000017" compartment_0000001 = 1.0; // initial value of $compartment_0000001 k1 = 6.6E-7; // initial value of k1 k10 = 1000.0; // initial value of k10 k11 = 2.5E8; // initial value of k11 k12 = 0.38; // initial value of k12 k13a = 0.0087; // initial value of k13a k13b = 0.0087; // initial value of k13b k17 = 30000.0; // initial value of k17 k18 = 7.0; // initial value of k18 k19 = 88000.0; // initial value of k19 k2 = 1.6E9; // initial value of k2 k3 = 1.6E9; // initial value of k3 k4 = 100000.0; // initial value of k4 k5 = 20000.0; // initial value of k5 k6 = 1.0; // initial value of k6 k7 = 3.4E7; // initial value of k7 k9 = 1000000.0; // initial value of k9 } /* * Model variables initial values */ protected double _compartment_0000001_species_0000016_; protected double _compartment_0000001_species_0000017_; protected double rate_fast; protected double rate_reaction_0; protected double rate_reaction_0000001; protected double rate_reaction_1; protected double rate_reaction_10; protected double rate_reaction_11; protected double rate_reaction_12; protected double rate_reaction_13; protected double rate_reaction_14; protected double rate_reaction_2; protected double rate_reaction_3; protected double rate_reaction_4; protected double rate_reaction_5; protected double rate_reaction_6; protected double rate_reaction_7; protected double rate_reaction_8; protected double rate_reaction_9; protected double compartment_0000001; protected double Cu_I_ZnSOD; protected double HO2star; protected double k1; protected double k10; protected double k11; protected double k12; protected double k13a; protected double k13b; protected double k17; protected double k18; protected double k19; protected double k2; protected double k3; protected double k4; protected double k5; protected double k6; protected double k7; protected double k9; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[9]; 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] = Cu_I_ZnSOD; y[8] = HO2star; return y; } public double[] getInitialValues() { double [] x = new double[7]; this.time = 0.0; x[0] = 0.0; // - $"compartment_0000001.species_0000001" x[1] = 5.0E-6; // - $"compartment_0000001.species_0000002" x[2] = 0.0; // - $"compartment_0000001.species_0000006" x[3] = 0.0; // - $"compartment_0000001.species_0000007" x[4] = 0.0; // - $"compartment_0000001.species_0000008" x[5] = 0.0; // - $"compartment_0000001.species_0000009" x[6] = 0.0; // - $"compartment_0000001.species_0000011" __internalVarInitFunc_0(time, x); __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) { __internalVarInitFunc_0(time, x); __internalRateVarInitFunc_0(time, x); } /* * calculate dy/dt for 'BIOMD0000000108.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate_fast+rate_reaction_0000001-rate_reaction_0-rate_reaction_1-rate_reaction_2-rate_reaction_3; result[1] = -rate_reaction_0+rate_reaction_10-rate_reaction_11+rate_reaction_1; result[2] = +rate_reaction_1-rate_reaction_3-rate_reaction_4-rate_reaction_5+rate_reaction_7; result[3] = +rate_reaction_12-rate_reaction_13-rate_reaction_14*2-rate_reaction_2; result[4] = +rate_reaction_3*2+rate_reaction_4*2-rate_reaction_6-rate_reaction_8; result[5] = +rate_reaction_13+rate_reaction_2-rate_reaction_9; result[6] = -rate_reaction_12+rate_reaction_13+rate_reaction_7+rate_reaction_8; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[7]; __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 ...