/* * This code is generated by BioUML FrameWork * for BIOMD0000000066.xml diagram at 2008.03.20 15:04:53 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000066 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_vak = compartment*(vak_vm11*(x[2]*x[4] - x[3]*x[0]/vak_keqak)/((vak_k11*(1 + Math.pow((x[9]/vak_k1thr), vak_nak1))/(1 + Math.pow((x[9]/(vak_alpha*vak_k1thr)), vak_nak1)) + vak_k11*x[3]/vak_k1aspp + x[2])*(vak_k1atp*(1 + x[0]/vak_k1adp) + x[4])) + vak_vm13*(x[2]*x[4] - x[3]*x[0]/vak_keqak)/((1 + Math.pow((vak_lys/vak_k1lys), vak_nak3))*(vak_k13*(1 + x[3]/vak_k13aspp) + x[2])*(vak_k13atp*(1 + x[0]/vak_k13adp) + x[4]))); rate_vasd = compartment*(vasd_vm2f*(x[3]*x[7] - x[1]*x[6]*x[8]/vasd_k2eq)/((vasd_k2aspp*(1 + x[1]/vasd_k2asa)*(1 + x[8]/vasd_k2p) + x[3])*(vasd_k2nadph*(1 + x[6]/vasd_k2nadp) + x[7]))); rate_vatpase = compartment*vatpase_prot*vatpase_katpase; rate_vhdh = compartment*(vhdh_vm3f*(x[1]*x[7] - x[10]*x[6]/vhdh_k3eq)/((1 + Math.pow((x[9]/vhdh_k3thr), vhdh_nhdh1))/(1 + Math.pow((x[9]/(vhdh_alpha3*vhdh_k3thr)), vhdh_nhdh1))*(vhdh_k3asa + x[1] + x[10]*vhdh_k3asa/vhdh_k3hs)*(vhdh_k3nadph*(1 + x[6]/vhdh_k3nadp) + x[7]))); rate_vhk = compartment*(vhk_vm4f*x[10]*x[4]/((1 + vhk_lys/vhk_k4lys)*(x[4] + vhk_k4atp*(1 + x[10]/vhk_k4ihs))*(x[10] + vhk_k4hs*(1 + x[9]/vhk_k4thr)*(1 + x[4]/vhk_k4iatp)))); rate_vnadph_endo = compartment*vnadph_endo_prot*vnadph_endo_knadph*x[7]; rate_vtsy = compartment*vtsy_vm5*x[5]/(x[5] + vtsy_k5hsp); } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ compartment = 1.0; // initial value of $compartment vak_alpha = 2.47; // initial value of vak_alpha vak_k11 = 0.97; // initial value of vak_k11 vak_k13 = 0.32; // initial value of vak_k13 vak_k13adp = 0.25; // initial value of vak_k13adp vak_k13aspp = 0.017; // initial value of vak_k13aspp vak_k13atp = 0.22; // initial value of vak_k13atp vak_k1adp = 0.25; // initial value of vak_k1adp vak_k1aspp = 0.017; // initial value of vak_k1aspp vak_k1atp = 0.98; // initial value of vak_k1atp vak_k1lys = 0.391; // initial value of vak_k1lys vak_k1thr = 0.167; // initial value of vak_k1thr vak_keqak = 6.4E-4; // initial value of vak_keqak vak_lys = 0.46; // initial value of vak_lys vak_nak1 = 4.09; // initial value of vak_nak1 vak_nak3 = 2.8; // initial value of vak_nak3 vak_vm11 = 0.15; // initial value of vak_vm11 vak_vm13 = 0.0722; // initial value of vak_vm13 vasd_k2asa = 0.11; // initial value of vasd_k2asa vasd_k2aspp = 0.022; // initial value of vasd_k2aspp vasd_k2eq = 56.4150334574039; // initial value of vasd_k2eq vasd_k2nadp = 0.144; // initial value of vasd_k2nadp vasd_k2nadph = 0.029; // initial value of vasd_k2nadph vasd_k2p = 10.0; // initial value of vasd_k2p vasd_vm2f = 0.1812; // initial value of vasd_vm2f vatpase_katpase = 4.1E-5; // initial value of vatpase_katpase vatpase_prot = 202.0; // initial value of vatpase_prot vhdh_alpha3 = 3.93; // initial value of vhdh_alpha3 vhdh_k3asa = 0.24; // initial value of vhdh_k3asa vhdh_k3eq = 3162.27766016838; // initial value of vhdh_k3eq vhdh_k3hs = 3.39; // initial value of vhdh_k3hs vhdh_k3nadp = 0.067; // initial value of vhdh_k3nadp vhdh_k3nadph = 0.037; // initial value of vhdh_k3nadph vhdh_k3thr = 0.097; // initial value of vhdh_k3thr vhdh_nhdh1 = 1.41; // initial value of vhdh_nhdh1 vhdh_vm3f = 1.001; // initial value of vhdh_vm3f vhk_k4atp = 0.072; // initial value of vhk_k4atp vhk_k4hs = 0.11; // initial value of vhk_k4hs vhk_k4iatp = 4.35; // initial value of vhk_k4iatp vhk_k4ihs = 4.7; // initial value of vhk_k4ihs vhk_k4lys = 9.45; // initial value of vhk_k4lys vhk_k4thr = 1.09; // initial value of vhk_k4thr vhk_lys = 0.46; // initial value of vhk_lys vhk_vm4f = 0.1; // initial value of vhk_vm4f vnadph_endo_knadph = 5.4E-6; // initial value of vnadph_endo_knadph vnadph_endo_prot = 202.0; // initial value of vnadph_endo_prot vtsy_k5hsp = 0.31; // initial value of vtsy_k5hsp vtsy_vm5 = 0.0434; // initial value of vtsy_vm5 } /* * Model variables initial values */ protected double rate_vak; protected double rate_vasd; protected double rate_vatpase; protected double rate_vhdh; protected double rate_vhk; protected double rate_vnadph_endo; protected double rate_vtsy; protected double compartment; protected double vak_alpha; protected double vak_k11; protected double vak_k13; protected double vak_k13adp; protected double vak_k13aspp; protected double vak_k13atp; protected double vak_k1adp; protected double vak_k1aspp; protected double vak_k1atp; protected double vak_k1lys; protected double vak_k1thr; protected double vak_keqak; protected double vak_lys; protected double vak_nak1; protected double vak_nak3; protected double vak_vm11; protected double vak_vm13; protected double vasd_k2asa; protected double vasd_k2aspp; protected double vasd_k2eq; protected double vasd_k2nadp; protected double vasd_k2nadph; protected double vasd_k2p; protected double vasd_vm2f; protected double vatpase_katpase; protected double vatpase_prot; protected double vhdh_alpha3; protected double vhdh_k3asa; protected double vhdh_k3eq; protected double vhdh_k3hs; protected double vhdh_k3nadp; protected double vhdh_k3nadph; protected double vhdh_k3thr; protected double vhdh_nhdh1; protected double vhdh_vm3f; protected double vhk_k4atp; protected double vhk_k4hs; protected double vhk_k4iatp; protected double vhk_k4ihs; protected double vhk_k4lys; protected double vhk_k4thr; protected double vhk_lys; protected double vhk_vm4f; protected double vnadph_endo_knadph; protected double vnadph_endo_prot; protected double vtsy_k5hsp; protected double vtsy_vm5; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[11]; 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]; return y; } public double[] getInitialValues() { double [] x = new double[11]; this.time = 0.0; x[0] = 0.0; // - $"compartment.adp" x[1] = 0.0; // - $"compartment.asa" x[2] = 2.0; // - $"compartment.asp" x[3] = 0.0; // - $"compartment.aspp" x[4] = 10.0; // - $"compartment.atp" x[5] = 0.0; // - $"compartment.hsp" x[6] = 0.0; // - $"compartment.nadp" x[7] = 2.0; // - $"compartment.nadph" x[8] = 0.0; // - $"compartment.phos" x[9] = 2.0; // - $"compartment.thr" x[10] = 0.0; // - $compartment.hs __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 'BIOMD0000000066.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = +rate_vak+rate_vatpase+rate_vhk; result[1] = +rate_vasd-rate_vhdh; result[2] = -rate_vak; result[3] = +rate_vak-rate_vasd; result[4] = -rate_vak-rate_vatpase-rate_vhk; result[5] = +rate_vhk-rate_vtsy; result[6] = +rate_vasd+rate_vhdh+rate_vnadph_endo; result[7] = -rate_vasd-rate_vhdh-rate_vnadph_endo; result[8] = +rate_vasd+rate_vatpase+rate_vtsy; result[9] = +rate_vtsy; result[10] = +rate_vhdh-rate_vhk; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[11]; __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 ...