/* * This code is generated by BioUML FrameWork * for BIOMD0000000085.xml diagram at 2008.03.20 15:08:06 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000085 extends JavaBaseModel { /* * Write rules to calculate equation parameters */ private void __internalVarInitFunc_0(double time, double[] x) { parameter_0 = (x[12] + x[2] + x[7] + x[3])/1.0E-8; parameter_1 = (25*x[7] + 25*x[3] + 0.013*x[2] + 0.013*x[12])/1.0E-8; } /* * Write rules to calculate equation parameters excluding internal variables. */ public void __internalRateVarInitFunc_0(double time, double[] x) { rate_reaction_1 = compartment_0*(reaction_1_k1*x[1]*x[10] - reaction_1_k2*x[12]); rate_reaction_10 = compartment_0*(reaction_10_k1*x[2] - reaction_10_k2*x[5]*x[14]); rate_reaction_11 = compartment_0*(reaction_11_k1*x[5] - reaction_11_k2*x[16]*x[15]); rate_reaction_13 = compartment_0*(reaction_13_k1*x[3] - reaction_13_k2*x[4]*x[14]); rate_reaction_14 = compartment_0*(reaction_14_k1*x[4] - reaction_14_k2*x[9]*x[15]); rate_reaction_16 = compartment_0*(reaction_16_k1*x[9]*x[11] - reaction_16_k2*x[6]); rate_reaction_17 = compartment_0*(reaction_17_k1*x[6]*x[10] - reaction_17_k2*x[7]); rate_reaction_19 = compartment_0*(reaction_19_k1*x[2]*x[0] - reaction_19_k2*x[7]); rate_reaction_20 = compartment_0*(reaction_20_k1*x[7] - reaction_20_k2*x[8]*x[14]); rate_reaction_23 = compartment_0*(reaction_23_k1*x[8] - reaction_23_k2*x[6]*x[15]); rate_reaction_3 = compartment_0*(reaction_3_k1*x[12] - reaction_3_k2*x[13]*x[14]); rate_reaction_4 = compartment_0*(reaction_4_k1*x[13] - reaction_4_k2*x[1]*x[15]); rate_reaction_5 = compartment_0*(reaction_5_k1*x[16]*x[10] - reaction_5_k2*x[2]); rate_reaction_6 = compartment_0*(reaction_6_k1*x[12]*x[11] - reaction_6_k2*x[2]); rate_reaction_7 = compartment_0*(reaction_7_k1*x[12]*x[0] - reaction_7_k2*x[3]); rate_reaction_8 = compartment_0*(reaction_8_k1*x[13]*x[0] - reaction_8_k2*x[4]); rate_reaction_9 = compartment_0*(reaction_9_k1*x[13]*x[11] - reaction_9_k2*x[5]); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ compartment_0 = 1.0; // initial value of $compartment_0 reaction_10_k1 = 0.013; // initial value of reaction_10_k1 reaction_10_k2 = 2.22E-9; // initial value of reaction_10_k2 reaction_11_k1 = 2.0; // initial value of reaction_11_k1 reaction_11_k2 = 1470000.0; // initial value of reaction_11_k2 reaction_13_k1 = 25.0; // initial value of reaction_13_k1 reaction_13_k2 = 0.244; // initial value of reaction_13_k2 reaction_14_k1 = 1.0E-4; // initial value of reaction_14_k1 reaction_14_k2 = 3.83; // initial value of reaction_14_k2 reaction_16_k1 = 3.96E9; // initial value of reaction_16_k1 reaction_16_k2 = 5.43E-5; // initial value of reaction_16_k2 reaction_17_k1 = 1620000.0; // initial value of reaction_17_k1 reaction_17_k2 = 0.00875; // initial value of reaction_17_k2 reaction_19_k1 = 6300000.0; // initial value of reaction_19_k1 reaction_19_k2 = 0.478; // initial value of reaction_19_k2 reaction_1_k1 = 529000.0; // initial value of reaction_1_k1 reaction_1_k2 = 8.38E-6; // initial value of reaction_1_k2 reaction_20_k1 = 25.0; // initial value of reaction_20_k1 reaction_20_k2 = 0.00297; // initial value of reaction_20_k2 reaction_23_k1 = 2.75; // initial value of reaction_23_k1 reaction_23_k2 = 2940.0; // initial value of reaction_23_k2 reaction_3_k1 = 0.013; // initial value of reaction_3_k1 reaction_3_k2 = 9.03E-7; // initial value of reaction_3_k2 reaction_4_k1 = 1.0E-4; // initial value of reaction_4_k1 reaction_4_k2 = 62.3; // initial value of reaction_4_k2 reaction_5_k1 = 853000.0; // initial value of reaction_5_k1 reaction_5_k2 = 0.00468; // initial value of reaction_5_k2 reaction_6_k1 = 1.32E8; // initial value of reaction_6_k1 reaction_6_k2 = 1.28; // initial value of reaction_6_k2 reaction_7_k1 = 386000.0; // initial value of reaction_7_k1 reaction_7_k2 = 0.0408; // initial value of reaction_7_k2 reaction_8_k1 = 64100.0; // initial value of reaction_8_k1 reaction_8_k2 = 0.95; // initial value of reaction_8_k2 reaction_9_k1 = 9.47E7; // initial value of reaction_9_k1 reaction_9_k2 = 0.00227; // initial value of reaction_9_k2 } /* * Model variables initial values */ protected double rate_reaction_1; protected double rate_reaction_10; protected double rate_reaction_11; protected double rate_reaction_13; protected double rate_reaction_14; protected double rate_reaction_16; protected double rate_reaction_17; protected double rate_reaction_19; protected double rate_reaction_20; protected double rate_reaction_23; 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_0; protected double parameter_0; protected double parameter_1; protected double reaction_10_k1; protected double reaction_10_k2; protected double reaction_11_k1; protected double reaction_11_k2; protected double reaction_13_k1; protected double reaction_13_k2; protected double reaction_14_k1; protected double reaction_14_k2; protected double reaction_16_k1; protected double reaction_16_k2; protected double reaction_17_k1; protected double reaction_17_k2; protected double reaction_19_k1; protected double reaction_19_k2; protected double reaction_1_k1; protected double reaction_1_k2; protected double reaction_20_k1; protected double reaction_20_k2; protected double reaction_23_k1; protected double reaction_23_k2; protected double reaction_3_k1; protected double reaction_3_k2; protected double reaction_4_k1; protected double reaction_4_k2; protected double reaction_5_k1; protected double reaction_5_k2; protected double reaction_6_k1; protected double reaction_6_k2; protected double reaction_7_k1; protected double reaction_7_k2; protected double reaction_8_k1; protected double reaction_8_k2; protected double reaction_9_k1; protected double reaction_9_k2; public double[] extendResult(double time,double [] x) { this.time = time; __internalVarInitFunc_0(time, x); double[] y = new double[19]; 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] = parameter_0; y[18] = parameter_1; return y; } public double[] getInitialValues() { double [] x = new double[17]; this.time = 0.0; x[0] = 0.0; // - $"compartment_0.species_0" x[1] = 1.0E-8; // - $"compartment_0.species_1" x[2] = 0.0; // - $"compartment_0.species_10" x[3] = 0.0; // - $"compartment_0.species_11" x[4] = 0.0; // - $"compartment_0.species_12" x[5] = 0.0; // - $"compartment_0.species_13" x[6] = 0.0; // - $"compartment_0.species_14" x[7] = 0.0; // - $"compartment_0.species_15" x[8] = 0.0; // - $"compartment_0.species_16" x[9] = 0.0; // - $"compartment_0.species_2" x[10] = 4.68E-4; // - $"compartment_0.species_3" x[11] = 1.0E-5; // - $"compartment_0.species_4" x[12] = 0.0; // - $"compartment_0.species_5" x[13] = 0.0; // - $"compartment_0.species_6" x[14] = 0.0044; // - $"compartment_0.species_7" x[15] = 1.49E-4; // - $"compartment_0.species_8" x[16] = 0.0; // - $"compartment_0.species_9" __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 'BIOMD0000000085.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate_reaction_19-rate_reaction_7-rate_reaction_8; result[1] = -rate_reaction_1+rate_reaction_4; result[2] = -rate_reaction_10-rate_reaction_19+rate_reaction_5+rate_reaction_6; result[3] = -rate_reaction_13+rate_reaction_7; result[4] = +rate_reaction_13-rate_reaction_14+rate_reaction_8; result[5] = +rate_reaction_10-rate_reaction_11+rate_reaction_9; result[6] = +rate_reaction_16-rate_reaction_17+rate_reaction_23; result[7] = +rate_reaction_17+rate_reaction_19-rate_reaction_20; result[8] = +rate_reaction_20-rate_reaction_23; result[9] = +rate_reaction_14-rate_reaction_16; result[10] = -rate_reaction_17-rate_reaction_1-rate_reaction_5; result[11] = -rate_reaction_16-rate_reaction_6-rate_reaction_9; result[12] = +rate_reaction_1-rate_reaction_3-rate_reaction_6-rate_reaction_7; result[13] = +rate_reaction_3-rate_reaction_4-rate_reaction_8-rate_reaction_9; result[14] = +rate_reaction_10+rate_reaction_13+rate_reaction_20+rate_reaction_3; result[15] = +rate_reaction_11+rate_reaction_14+rate_reaction_23+rate_reaction_4; result[16] = +rate_reaction_11-rate_reaction_5; } 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 ...