/* * This code is generated by BioUML FrameWork * for BIOMD0000000088.xml diagram at 2008.03.20 15:08:18 */ import biouml.plugins.simulation.ae.NewtonSolver; import biouml.plugins.simulation.java.JavaBaseModel; import ru.biosoft.math.MathRoutines; public class BIOMD0000000088 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_re1 = c0_c1*((1 + re1_ratio)*re1_Vmax*x[3]*c0_s2/re1_Km - re1_Vmax*re1_ratio*x[11]); rate_re100 = c0_c1*(re100_kf*x[4]*x[4]*x[54] - re100_kb*x[65]); rate_re101 = c0_c1*(re101_kf*x[88]*x[6] - re101_kb*x[87]); rate_re102 = c0_c1*(re102_kf*x[87] - re102_kb*x[34]); rate_re106 = c0_c1*re106_kf*x[34]; rate_re107 = c0_c1*re107_kf*x[33]; rate_re108 = c0_c1*re108_kf*x[31]; rate_re109 = c0_c1*((1 + re109_ratio)*re109_Vmax*x[55]*x[4]/re109_Km - re109_Vmax*re109_ratio*x[66]); rate_re110 = c0_c1*((1 + re110_ratio)*re110_Vmax*x[34]*x[41]/re110_Km - re110_Vmax*re110_ratio*x[40]); rate_re111 = c0_c1*((1 + re111_ratio)*re111_Vmax*x[33]*x[41]/re111_Km - re111_ratio*re111_Vmax*x[39]); rate_re112 = c0_c1*((1 + re112_ratio)*re112_Vmax*x[31]*x[41]/re112_Km - re112_Vmax*re112_ratio*x[38]); rate_re113 = c0_c1*re113_Vmax*x[40]; rate_re114 = c0_c1*re114_Vmax*x[39]; rate_re115 = c0_c1*re115_Vmax*x[38]; rate_re116 = c0_c1*re116_kf*x[42]; rate_re117 = c0_c1*(re117_kf*x[43]*x[42] - re117_kb*x[44]); rate_re118 = c0_c1*(re118_kf*x[43]*x[41] - re118_kb*x[45]); rate_re119 = c0_c1*re119_kf*x[44]; rate_re12 = c0_c1*re12_kf*_c0_c1_s48_*x[56]; rate_re120 = c0_c1*((1 + re120_ratio)*re120_Vmax*x[2]*x[46]/re120_Km - re120_Vmax*re120_ratio*x[49]); rate_re121 = c0_c1*((1 + re121_ratio)*re121_Vmax*x[2]*x[47]/re121_Km - re121_Vmax*re121_ratio*x[50]); rate_re123 = c0_c1*re123_Vmax*x[49]; rate_re124 = c0_c1*re124_Vmax*x[50]; rate_re125 = c0_c1*((1 + re125_ratio)*re125_Vmax*x[19]*x[46]/re125_Km - re125_Vmax*re125_ratio*x[68]); rate_re126 = c0_c1*((1 + re126_ratio)*re126_Vmax*x[19]*x[47]/re126_Km - re126_Vmax*re126_ratio*x[67]); rate_re127 = c0_c1*re127_Vmax*x[68]; rate_re128 = c0_c1*re128_Vmax*x[67]; rate_re129 = c0_c1*((1 + re129_ratio)*re129_Vmax*x[2]*x[43]/re129_Km - re129_Vmax*re129_ratio*x[69]); rate_re130 = c0_c1*re130_Vmax*x[69]; rate_re131 = c0_c1*((1 + re131_ratio)*re131_Vmax*x[19]*x[43]/re131_Km - re131_Vmax*re131_ratio*x[76]); rate_re132 = c0_c1*re132_Vmax*x[76]; rate_re133 = c0_c1*((1 + re133_ratio)*re133_Vmax*x[48]*x[93]/re133_Km - re133_Vmax*re133_ratio*x[70]); rate_re134 = c0_c1*((1 + re134_ratio)*re134_Vmax*x[48]*x[43]/re134_Km - re134_Vmax*re134_ratio*x[71]); rate_re135 = c0_c1*((1 + re135_ratio)*re135_Vmax*x[47]*x[93]/re135_Km - re135_Vmax*re135_ratio*x[72]); rate_re136 = c0_c1*((1 + re136_ratio)*re136_Vmax*x[43]*x[47]/re136_Km - re136_Vmax*re136_ratio*x[73]); rate_re137 = c0_c1*re137_Vmax*x[70]; rate_re138 = c0_c1*re138_Vmax*x[71]; rate_re139 = c0_c1*re139_Vmax*x[72]; rate_re14 = c0_c1*re14_kf*x[84]; rate_re140 = c0_c1*re140_Vmax*x[73]; } public void __internalRateVarInitFunc_1(double time, double[] x) { rate_re141 = c0_c1*re141_kf*x[93]; rate_re15 = c0_c1*(re15_kf*x[63]*x[92] - re15_kb*x[62]); rate_re154 = c0_c1*((1 + re154_ratio)*re154_Vmax*x[25]*x[46]/re154_Km - re154_Vmax*re154_ratio*x[74]); rate_re155 = c0_c1*((1 + re155_ratio)*re155_Vmax*x[25]*x[47]/re155_Km - re155_Vmax*re155_ratio*x[75]); rate_re156 = c0_c1*re156_Vmax*x[74]; rate_re157 = c0_c1*re157_Vmax*x[75]; rate_re158 = c0_c1*((1 + re158_ratio)*re158_Vmax*x[26]*x[46]/re158_Km - re158_Vmax*re158_ratio*x[85]); rate_re159 = c0_c1*((1 + re159_ratio)*re159_Vmax*x[27]*x[46]/re159_Km - re159_Vmax*re159_ratio*x[82]); rate_re16 = c0_c1*re16_kf*_c0_c1_s48_*x[62]; rate_re160 = c0_c1*((1 + re160_ratio)*re160_Vmax*x[28]*x[46]/re160_Km - re160_Vmax*re160_ratio*x[80]); rate_re161 = c0_c1*((1 + re161_ratio)*re161_Vmax*x[29]*x[46]/re161_Km - re161_Vmax*re161_ratio*x[79]); rate_re162 = c0_c1*((1 + re162_ratio)*re162_Vmax*x[26]*x[47]/re162_Km - re162_Vmax*re162_ratio*x[83]); rate_re163 = c0_c1*((1 + re163_ratio)*re163_Vmax*x[27]*x[47]/re163_Km - re163_Vmax*re163_ratio*x[81]); rate_re164 = c0_c1*((1 + re164_ratio)*re164_Vmax*x[28]*x[47]/re164_Km - re164_Vmax*re164_ratio*x[78]); rate_re165 = c0_c1*((1 + re165_ratio)*re165_Vmax*x[29]*x[47]/re165_Km - re165_Vmax*re165_ratio*x[77]); rate_re166 = c0_c1*re166_Vmax*x[77]; rate_re167 = c0_c1*re167_Vmax*x[79]; rate_re168 = c0_c1*re168_Vmax*x[78]; rate_re169 = c0_c1*re169_Vmax*x[80]; rate_re17 = c0_c1*re17_kf*x[60]; rate_re170 = c0_c1*re170_Vmax*x[81]; rate_re171 = c0_c1*re171_Vmax*x[82]; rate_re172 = c0_c1*re172_Vmax*x[83]; rate_re173 = c0_c1*re173_Vmax*x[85]; rate_re174 = c0_c1*re174_g*_c0_c1_s556_*(_c0_s267_ - x[4]); rate_re175 = c0_c1*re175_g*_c0_c1_s557_*(x[0]/0.1 - x[4]); rate_re19 = c0_c1*re19_kf*x[51]*x[59]; rate_re20 = c0_c1*((1 + re20_ratio)*re20_Vmax*x[14]*x[94]/re20_Km - re20_ratio*re20_Vmax*x[13]); rate_re22 = c0_c1*re22_kf*x[52]*x[61]; rate_re23 = c0_c1*(re23_kf*x[60]*x[95] - re23_kb*x[57]); rate_re24 = c0_c1*(re24_Vmax*x[17]*x[57]/(re24_Km + x[16])); rate_re26 = c0_c1*((1 + re26_ratio)*re26_Vmax*x[95]*x[17]/re26_Km - re26_Vmax*re26_ratio*x[18]); rate_re28 = c0_c1*((1 + re28_ratio)*re28_Vmax*x[1]*x[16]/re28_Km - re28_Vmax*re28_ratio*x[15]); rate_re32 = c0_c1*re32_Vmax*x[18]; rate_re33 = c0_c1*re33_Vmax*x[15]; rate_re34 = c0_c1*re34_Vmax*x[13]; rate_re37 = c0_c1*re37_kf*x[57]; rate_re38 = c0_c1*re38_kf*x[16]; rate_re39 = c0_c1*(re39_kf*x[2]*x[16] - re39_kb*x[19]); rate_re40 = c0_c1*re40_Vmax*x[11]; } public void __internalRateVarInitFunc_2(double time, double[] x) { rate_re43 = c0_c1*(re43_kf*x[58]*x[92] - re43_kb*x[56]); rate_re44 = c0_c1*re44_kf*x[14]; rate_re45 = c0_c1*re45_kf*x[92]; rate_re47 = c0_c1*(re47_kf*x[14]*x[91] - re47_kb*x[86]); rate_re48 = c0_c1*(re48_kf*x[53]*x[14] - re48_kb*x[64]); rate_re51 = c0_c1*(re51_kf*x[4]*x[64] - re51_kb*x[86]); rate_re52 = c0_c1*(re52_kf*x[53]*x[4] - re52_kb*x[91]); rate_re54 = c0_c1*re54_kf*x[86]; rate_re55 = c0_c1*((1 + re55_ratio)*re55_Vmax*x[91]*_c0_c1_s151_/re55_Km - re55_ratio*re55_Vmax*x[90]); rate_re56 = c0_c1*((1 + re56_ratio)*re56_Vmax*x[86]*_c0_c1_s151_/re56_Km - re56_ratio*re56_Vmax*x[89]); rate_re57 = c0_c1*re57_Vmax*x[90]; rate_re58 = c0_c1*re58_Vmax*x[89]; rate_re59 = c0_c1*re59_kf*x[6]; rate_re60 = c0_c1*re60_kf*x[5]; rate_re68 = c0_c1*(re68_kf*x[5]*x[5]*x[5]*x[9] - re68_kb*x[10]); rate_re73 = c0_c1*re73_g*x[10]*(x[0]/0.1 - x[4]); rate_re85 = c0_c1*re85_kf*x[65]; rate_re86 = c0_c1*(re86_kf*x[20]*x[4] - re86_kb*x[21]); rate_re87 = c0_c1*(re87_kf*x[21]*x[4] - re87_kb*x[22]); rate_re88 = c0_c1*(re88_kf*x[23]*x[4] - re88_kb*x[24]); rate_re89 = c0_c1*(re89_kf*x[22]*x[4] - re89_kb*x[23]); rate_re90 = c0_c1*(re90_kf*x[24]*x[25] - re90_kb*x[29]); rate_re91 = c0_c1*(re91_kf*x[23]*x[25] - re91_kb*x[28]); rate_re92 = c0_c1*(re92_kf*x[22]*x[25] - re92_kb*x[27]); rate_re93 = c0_c1*(re93_kf*x[21]*x[25] - re93_kb*x[26]); rate_re94 = c0_c1*(re94_kf*x[30] - re94_kb*x[31]); rate_re95 = c0_c1*(re95_kf*x[30]*x[6] - re95_kb*x[32]); rate_re96 = c0_c1*(re96_kf*x[88] - re96_kb*x[33]); rate_re97 = c0_c1*(re97_kf*x[30]*x[4] - re97_kb*x[88]); rate_re98 = c0_c1*re98_Vmax*x[66]; } public void Init() { initialValues = getInitialValues(); /* * Initialize variables */ _c0_c1_s151_ = 10.0; // initial value of $"c0.c1.s151" _c0_c1_s48_ = 50.0; // initial value of $"c0.c1.s48" _c0_c1_s50_ = 5.0; // initial value of $"c0.c1.s50" _c0_c1_s556_ = 0.00833; // initial value of $"c0.c1.s556" _c0_c1_s557_ = 0.0010; // initial value of $"c0.c1.s557" _c0_s267_ = 4000.0; // initial value of $"c0.s267" c0_c1 = 1.0; // initial value of $c0.c1 re100_kb = 3.0; // initial value of re100_kb re100_kf = 30.0; // initial value of re100_kf re101_kb = 8.6348; // initial value of re101_kb re101_kf = 0.0040; // initial value of re101_kf re102_kb = 0.1; // initial value of re102_kb re102_kf = 1.0; // initial value of re102_kf re106_kf = 4.63E-5; // initial value of re106_kf re107_kf = 4.63E-5; // initial value of re107_kf re108_kf = 4.63E-5; // initial value of re108_kf re109_Km = 0.04; // initial value of re109_Km re109_Vmax = 4.9; // initial value of re109_Vmax re109_ratio = 4.0; // initial value of re109_ratio re110_Km = 0.0014; // initial value of re110_Km re110_Vmax = 3.94; // initial value of re110_Vmax re110_ratio = 4.0; // initial value of re110_ratio re111_Km = 0.0014; // initial value of re111_Km re111_Vmax = 3.94; // initial value of re111_Vmax re111_ratio = 4.0; // initial value of re111_ratio re112_Km = 0.0014; // initial value of re112_Km re112_Vmax = 3.94; // initial value of re112_Vmax re112_ratio = 4.0; // initial value of re112_ratio re113_Vmax = 3.94; // initial value of re113_Vmax re114_Vmax = 3.94; // initial value of re114_Vmax re115_Vmax = 3.94; // initial value of re115_Vmax re116_kf = 0.5; // initial value of re116_kf re117_kb = 0.62; // initial value of re117_kb re117_kf = 100.0; // initial value of re117_kf re118_kb = 0.1; // initial value of re118_kb re118_kf = 0.01; // initial value of re118_kf re119_kf = 0.5; // initial value of re119_kf re120_Km = 4.5099; // initial value of re120_Km re120_Vmax = 1.28; // initial value of re120_Vmax re120_ratio = 16.617; // initial value of re120_ratio re121_Km = 4.5099; // initial value of re121_Km re121_Vmax = 1.28; // initial value of re121_Vmax re121_ratio = 16.617; // initial value of re121_ratio re123_Vmax = 1.28; // initial value of re123_Vmax re124_Vmax = 1.28; // initial value of re124_Vmax re125_Km = 2.47; // initial value of re125_Km re125_Vmax = 8.66; // initial value of re125_Vmax re125_ratio = 0.4261; // initial value of re125_ratio re126_Km = 2.47; // initial value of re126_Km re126_Vmax = 8.66; // initial value of re126_Vmax re126_ratio = 0.4261; // initial value of re126_ratio re127_Vmax = 8.66; // initial value of re127_Vmax re128_Vmax = 8.66; // initial value of re128_Vmax re129_Km = 0.18; // initial value of re129_Km re129_Vmax = 1.46; // initial value of re129_Vmax re129_ratio = 0.23288; // initial value of re129_ratio re12_kf = 0.01; // initial value of re12_kf re130_Vmax = 1.46; // initial value of re130_Vmax re131_Km = 0.1; // initial value of re131_Km re131_Vmax = 17.505; // initial value of re131_Vmax re131_ratio = 0.028278; // initial value of re131_ratio re132_Vmax = 17.505; // initial value of re132_Vmax re133_Km = 58.099; // initial value of re133_Km re133_Vmax = 1.95; // initial value of re133_Vmax re133_ratio = 28.795; // initial value of re133_ratio re134_Km = 16.0; // initial value of re134_Km re134_Vmax = 9.317; // initial value of re134_Vmax re134_ratio = 7.5865; // initial value of re134_ratio re135_Km = 58.099; // initial value of re135_Km re135_Vmax = 1.95; // initial value of re135_Vmax re135_ratio = 28.795; // initial value of re135_ratio re136_Km = 16.0; // initial value of re136_Km re136_Vmax = 9.317; // initial value of re136_Vmax re136_ratio = 7.5865; // initial value of re136_ratio re137_Vmax = 1.95; // initial value of re137_Vmax re138_Vmax = 9.317; // initial value of re138_Vmax re139_Vmax = 1.95; // initial value of re139_Vmax re140_Vmax = 9.317; // initial value of re140_Vmax re141_kf = 0.2; // initial value of re141_kf re14_kf = 0.00224; // initial value of re14_kf re154_Km = 148.08; // initial value of re154_Km re154_Vmax = 3.67; // initial value of re154_Vmax re154_ratio = 39.349; // initial value of re154_ratio re155_Km = 148.08; // initial value of re155_Km re155_Vmax = 3.67; // initial value of re155_Vmax re155_ratio = 39.349; // initial value of re155_ratio re156_Vmax = 3.67; // initial value of re156_Vmax re157_Vmax = 3.67; // initial value of re157_Vmax re158_Km = 10.019; // initial value of re158_Km re158_Vmax = 3.67; // initial value of re158_Vmax re158_ratio = 1.7299; // initial value of re158_ratio re159_Km = 10.019; // initial value of re159_Km re159_Vmax = 3.67; // initial value of re159_Vmax re159_ratio = 1.7299; // initial value of re159_ratio re15_kb = 0.0060; // initial value of re15_kb re15_kf = 1.0; // initial value of re15_kf re160_Km = 10.019; // initial value of re160_Km re160_Vmax = 3.67; // initial value of re160_Vmax re160_ratio = 1.7299; // initial value of re160_ratio re161_Km = 10.019; // initial value of re161_Km re161_Vmax = 3.67; // initial value of re161_Vmax re161_ratio = 1.7299; // initial value of re161_ratio re162_Km = 10.019; // initial value of re162_Km re162_Vmax = 3.67; // initial value of re162_Vmax re162_ratio = 1.7299; // initial value of re162_ratio re163_Km = 10.019; // initial value of re163_Km re163_Vmax = 3.67; // initial value of re163_Vmax re163_ratio = 1.7299; // initial value of re163_ratio re164_Km = 10.019; // initial value of re164_Km re164_Vmax = 3.67; // initial value of re164_Vmax re164_ratio = 1.7299; // initial value of re164_ratio re165_Km = 10.019; // initial value of re165_Km re165_Vmax = 3.67; // initial value of re165_Vmax re165_ratio = 1.7299; // initial value of re165_ratio re166_Vmax = 3.67; // initial value of re166_Vmax re167_Vmax = 3.67; // initial value of re167_Vmax re168_Vmax = 3.67; // initial value of re168_Vmax re169_Vmax = 3.67; // initial value of re169_Vmax re16_kf = 0.01; // initial value of re16_kf re170_Vmax = 3.67; // initial value of re170_Vmax re171_Vmax = 3.67; // initial value of re171_Vmax re172_Vmax = 3.67; // initial value of re172_Vmax re173_Vmax = 3.67; // initial value of re173_Vmax re174_g = 0.01; // initial value of re174_g re175_g = 0.01; // initial value of re175_g re17_kf = 0.0133; // initial value of re17_kf re19_kf = 0.01; // initial value of re19_kf re1_Km = 5.0; // initial value of re1_Km re1_Vmax = 15.0; // initial value of re1_Vmax re1_ratio = 4.0; // initial value of re1_ratio re20_Km = 0.05; // initial value of re20_Km re20_Vmax = 0.0102; // initial value of re20_Vmax re20_ratio = 23.51; // initial value of re20_ratio re22_kf = 0.01; // initial value of re22_kf re23_kb = 0.1; // initial value of re23_kb re23_kf = 20.0; // initial value of re23_kf re24_Km = 0.015; // initial value of re24_Km re24_Vmax = 0.052; // initial value of re24_Vmax re26_Km = 2.0; // initial value of re26_Km re26_Vmax = 0.04; // initial value of re26_Vmax re26_ratio = 4.0; // initial value of re26_ratio re28_Km = 2.83; // initial value of re28_Km re28_Vmax = 0.993; // initial value of re28_Vmax re28_ratio = 13.246; // initial value of re28_ratio re32_Vmax = 0.04; // initial value of re32_Vmax re33_Vmax = 0.9933; // initial value of re33_Vmax re34_Vmax = 0.0102; // initial value of re34_Vmax re37_kf = 0.0117; // initial value of re37_kf re38_kf = 3.667E-4; // initial value of re38_kf re39_kb = 0.5; // initial value of re39_kb re39_kf = 10.0; // initial value of re39_kf re40_Vmax = 15.0; // initial value of re40_Vmax re43_kb = 0.0060; // initial value of re43_kb re43_kf = 1.0; // initial value of re43_kf re44_kf = 0.0133; // initial value of re44_kf re45_kf = 0.00224; // initial value of re45_kf re47_kb = 1.0; // initial value of re47_kb re47_kf = 25.201; // initial value of re47_kf re48_kb = 1.0; // initial value of re48_kb re48_kf = 2.5201; // initial value of re48_kf re51_kb = 1.0; // initial value of re51_kb re51_kf = 30.0; // initial value of re51_kf re52_kb = 1.0; // initial value of re52_kb re52_kf = 3.0; // initial value of re52_kf re54_kf = 0.0133; // initial value of re54_kf re55_Km = 19.841; // initial value of re55_Km re55_Vmax = 10.0; // initial value of re55_Vmax re55_ratio = 4.0; // initial value of re55_ratio re56_Km = 5.0; // initial value of re56_Km re56_Vmax = 48.0; // initial value of re56_Vmax re56_ratio = 4.0; // initial value of re56_ratio re57_Vmax = 10.0; // initial value of re57_Vmax re58_Vmax = 48.0; // initial value of re58_Vmax re59_kf = 0.15; // initial value of re59_kf re60_kf = 2.5; // initial value of re60_kf re68_kb = 10.0; // initial value of re68_kb re68_kf = 0.1; // initial value of re68_kf re73_g = 150.0; // initial value of re73_g re85_kf = 1.0; // initial value of re85_kf re86_kb = 50.0; // initial value of re86_kb re86_kf = 10.0; // initial value of re86_kf re87_kb = 45.0; // initial value of re87_kb re87_kf = 10.0; // initial value of re87_kf re88_kb = 500.0; // initial value of re88_kb re88_kf = 10.0; // initial value of re88_kf re89_kb = 170.0; // initial value of re89_kb re89_kf = 10.0; // initial value of re89_kf re90_kb = 0.01; // initial value of re90_kb re90_kf = 10.0; // initial value of re90_kf re91_kb = 0.01; // initial value of re91_kb re91_kf = 10.0; // initial value of re91_kf re92_kb = 0.45; // initial value of re92_kb re92_kf = 0.1; // initial value of re92_kf re93_kb = 0.5; // initial value of re93_kb re93_kf = 0.1; // initial value of re93_kf re94_kb = 50.0; // initial value of re94_kb re94_kf = 1.0; // initial value of re94_kf re95_kb = 0.1; // initial value of re95_kb re95_kf = 3.0E-4; // initial value of re95_kf re96_kb = 3.5026; // initial value of re96_kb re96_kf = 1.2705; // initial value of re96_kf re97_kb = 0.5; // initial value of re97_kb re97_kf = 0.3; // initial value of re97_kf re98_Vmax = 4.9; // initial value of re98_Vmax } /* * Model variables initial values */ protected double _c0_c1_s151_; protected double _c0_c1_s48_; protected double _c0_c1_s50_; protected double _c0_c1_s556_; protected double _c0_c1_s557_; protected double _c0_s267_; protected double rate_re1; protected double rate_re100; protected double rate_re101; protected double rate_re102; protected double rate_re106; protected double rate_re107; protected double rate_re108; protected double rate_re109; protected double rate_re110; protected double rate_re111; protected double rate_re112; protected double rate_re113; protected double rate_re114; protected double rate_re115; protected double rate_re116; protected double rate_re117; protected double rate_re118; protected double rate_re119; protected double rate_re12; protected double rate_re120; protected double rate_re121; protected double rate_re123; protected double rate_re124; protected double rate_re125; protected double rate_re126; protected double rate_re127; protected double rate_re128; protected double rate_re129; protected double rate_re130; protected double rate_re131; protected double rate_re132; protected double rate_re133; protected double rate_re134; protected double rate_re135; protected double rate_re136; protected double rate_re137; protected double rate_re138; protected double rate_re139; protected double rate_re14; protected double rate_re140; protected double rate_re141; protected double rate_re15; protected double rate_re154; protected double rate_re155; protected double rate_re156; protected double rate_re157; protected double rate_re158; protected double rate_re159; protected double rate_re16; protected double rate_re160; protected double rate_re161; protected double rate_re162; protected double rate_re163; protected double rate_re164; protected double rate_re165; protected double rate_re166; protected double rate_re167; protected double rate_re168; protected double rate_re169; protected double rate_re17; protected double rate_re170; protected double rate_re171; protected double rate_re172; protected double rate_re173; protected double rate_re174; protected double rate_re175; protected double rate_re19; protected double rate_re20; protected double rate_re22; protected double rate_re23; protected double rate_re24; protected double rate_re26; protected double rate_re28; protected double rate_re32; protected double rate_re33; protected double rate_re34; protected double rate_re37; protected double rate_re38; protected double rate_re39; protected double rate_re40; protected double rate_re43; protected double rate_re44; protected double rate_re45; protected double rate_re47; protected double rate_re48; protected double rate_re51; protected double rate_re52; protected double rate_re54; protected double rate_re55; protected double rate_re56; protected double rate_re57; protected double rate_re58; protected double rate_re59; protected double rate_re60; protected double rate_re68; protected double rate_re73; protected double rate_re85; protected double rate_re86; protected double rate_re87; protected double rate_re88; protected double rate_re89; protected double rate_re90; protected double rate_re91; protected double rate_re92; protected double rate_re93; protected double rate_re94; protected double rate_re95; protected double rate_re96; protected double rate_re97; protected double rate_re98; protected double c0_c1; protected double c0_s2; protected double re100_kb; protected double re100_kf; protected double re101_kb; protected double re101_kf; protected double re102_kb; protected double re102_kf; protected double re106_kf; protected double re107_kf; protected double re108_kf; protected double re109_Km; protected double re109_Vmax; protected double re109_ratio; protected double re110_Km; protected double re110_Vmax; protected double re110_ratio; protected double re111_Km; protected double re111_Vmax; protected double re111_ratio; protected double re112_Km; protected double re112_Vmax; protected double re112_ratio; protected double re113_Vmax; protected double re114_Vmax; protected double re115_Vmax; protected double re116_kf; protected double re117_kb; protected double re117_kf; protected double re118_kb; protected double re118_kf; protected double re119_kf; protected double re120_Km; protected double re120_Vmax; protected double re120_ratio; protected double re121_Km; protected double re121_Vmax; protected double re121_ratio; protected double re123_Vmax; protected double re124_Vmax; protected double re125_Km; protected double re125_Vmax; protected double re125_ratio; protected double re126_Km; protected double re126_Vmax; protected double re126_ratio; protected double re127_Vmax; protected double re128_Vmax; protected double re129_Km; protected double re129_Vmax; protected double re129_ratio; protected double re12_kf; protected double re130_Vmax; protected double re131_Km; protected double re131_Vmax; protected double re131_ratio; protected double re132_Vmax; protected double re133_Km; protected double re133_Vmax; protected double re133_ratio; protected double re134_Km; protected double re134_Vmax; protected double re134_ratio; protected double re135_Km; protected double re135_Vmax; protected double re135_ratio; protected double re136_Km; protected double re136_Vmax; protected double re136_ratio; protected double re137_Vmax; protected double re138_Vmax; protected double re139_Vmax; protected double re140_Vmax; protected double re141_kf; protected double re14_kf; protected double re154_Km; protected double re154_Vmax; protected double re154_ratio; protected double re155_Km; protected double re155_Vmax; protected double re155_ratio; protected double re156_Vmax; protected double re157_Vmax; protected double re158_Km; protected double re158_Vmax; protected double re158_ratio; protected double re159_Km; protected double re159_Vmax; protected double re159_ratio; protected double re15_kb; protected double re15_kf; protected double re160_Km; protected double re160_Vmax; protected double re160_ratio; protected double re161_Km; protected double re161_Vmax; protected double re161_ratio; protected double re162_Km; protected double re162_Vmax; protected double re162_ratio; protected double re163_Km; protected double re163_Vmax; protected double re163_ratio; protected double re164_Km; protected double re164_Vmax; protected double re164_ratio; protected double re165_Km; protected double re165_Vmax; protected double re165_ratio; protected double re166_Vmax; protected double re167_Vmax; protected double re168_Vmax; protected double re169_Vmax; protected double re16_kf; protected double re170_Vmax; protected double re171_Vmax; protected double re172_Vmax; protected double re173_Vmax; protected double re174_g; protected double re175_g; protected double re17_kf; protected double re19_kf; protected double re1_Km; protected double re1_Vmax; protected double re1_ratio; protected double re20_Km; protected double re20_Vmax; protected double re20_ratio; protected double re22_kf; protected double re23_kb; protected double re23_kf; protected double re24_Km; protected double re24_Vmax; protected double re26_Km; protected double re26_Vmax; protected double re26_ratio; protected double re28_Km; protected double re28_Vmax; protected double re28_ratio; protected double re32_Vmax; protected double re33_Vmax; protected double re34_Vmax; protected double re37_kf; protected double re38_kf; protected double re39_kb; protected double re39_kf; protected double re40_Vmax; protected double re43_kb; protected double re43_kf; protected double re44_kf; protected double re45_kf; protected double re47_kb; protected double re47_kf; protected double re48_kb; protected double re48_kf; protected double re51_kb; protected double re51_kf; protected double re52_kb; protected double re52_kf; protected double re54_kf; protected double re55_Km; protected double re55_Vmax; protected double re55_ratio; protected double re56_Km; protected double re56_Vmax; protected double re56_ratio; protected double re57_Vmax; protected double re58_Vmax; protected double re59_kf; protected double re60_kf; protected double re68_kb; protected double re68_kf; protected double re73_g; protected double re85_kf; protected double re86_kb; protected double re86_kf; protected double re87_kb; protected double re87_kf; protected double re88_kb; protected double re88_kf; protected double re89_kb; protected double re89_kf; protected double re90_kb; protected double re90_kf; protected double re91_kb; protected double re91_kf; protected double re92_kb; protected double re92_kf; protected double re93_kb; protected double re93_kf; protected double re94_kb; protected double re94_kf; protected double re95_kb; protected double re95_kf; protected double re96_kb; protected double re96_kf; protected double re97_kb; protected double re97_kf; protected double re98_Vmax; protected double time; public double[] extendResult(double time,double [] x) { this.time = time; double[] y = new double[98]; 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]; y[23] = x[23]; y[24] = x[24]; y[25] = x[25]; y[26] = x[26]; y[27] = x[27]; y[28] = x[28]; y[29] = x[29]; y[30] = x[30]; y[31] = x[31]; y[32] = x[32]; y[33] = x[33]; y[34] = x[34]; y[35] = x[35]; y[36] = x[36]; y[37] = x[37]; y[38] = x[38]; y[39] = x[39]; y[40] = x[40]; y[41] = x[41]; y[42] = x[42]; y[43] = x[43]; y[44] = x[44]; y[45] = x[45]; y[46] = x[46]; y[47] = x[47]; y[48] = x[48]; y[49] = x[49]; y[50] = x[50]; y[51] = x[51]; y[52] = x[52]; y[53] = x[53]; y[54] = x[54]; y[55] = x[55]; y[56] = x[56]; y[57] = x[57]; y[58] = x[58]; y[59] = x[59]; y[60] = x[60]; y[61] = x[61]; y[62] = x[62]; y[63] = x[63]; y[64] = x[64]; y[65] = x[65]; y[66] = x[66]; y[67] = x[67]; y[68] = x[68]; y[69] = x[69]; y[70] = x[70]; y[71] = x[71]; y[72] = x[72]; y[73] = x[73]; y[74] = x[74]; y[75] = x[75]; y[76] = x[76]; y[77] = x[77]; y[78] = x[78]; y[79] = x[79]; y[80] = x[80]; y[81] = x[81]; y[82] = x[82]; y[83] = x[83]; y[84] = x[84]; y[85] = x[85]; y[86] = x[86]; y[87] = x[87]; y[88] = x[88]; y[89] = x[89]; y[90] = x[90]; y[91] = x[91]; y[92] = x[92]; y[93] = x[93]; y[94] = x[94]; y[95] = x[95]; y[96] = c0_s2; y[97] = x[96]; return y; } public double[] getInitialValues() { double [] x = new double[97]; this.time = 0.0; x[0] = 15.5; // - $"c0.c1.c2.s172" x[1] = 0.1; // - $"c0.c1.s118" x[2] = 0.042; // - $"c0.c1.s124" x[3] = 0.42; // - $"c0.c1.s130" x[4] = 0.0833; // - $"c0.c1.s135" x[5] = 0.3; // - $"c0.c1.s152" x[6] = 0.0; // - $"c0.c1.s153" x[7] = 0.0; // - $"c0.c1.s164" x[8] = 0.0; // - $"c0.c1.s165" x[9] = 0.008333; // - $"c0.c1.s171" x[10] = 0.0; // - $"c0.c1.s173" x[11] = 0.0; // - $"c0.c1.s174" x[12] = 0.0; // - $"c0.c1.s183" x[13] = 0.0; // - $"c0.c1.s184" x[14] = 0.0; // - $"c0.c1.s187" x[15] = 0.0; // - $"c0.c1.s213" x[16] = 0.0050; // - $"c0.c1.s214" x[17] = 0.09; // - $"c0.c1.s231" x[18] = 0.0; // - $"c0.c1.s233" x[19] = 0.0050; // - $"c0.c1.s252" x[20] = 19.65; // - $"c0.c1.s276" x[21] = 0.3; // - $"c0.c1.s277" x[22] = 0.0; // - $"c0.c1.s278" x[23] = 0.0; // - $"c0.c1.s279" x[24] = 0.0; // - $"c0.c1.s280" x[25] = 0.69; // - $"c0.c1.s289" x[26] = 0.05; // - $"c0.c1.s292" x[27] = 0.0; // - $"c0.c1.s293" x[28] = 0.0; // - $"c0.c1.s294" x[29] = 0.0; // - $"c0.c1.s295" x[30] = 2.0; // - $"c0.c1.s309" x[31] = 0.039823; // - $"c0.c1.s310" x[32] = 0.0; // - $"c0.c1.s311" x[33] = 0.68193; // - $"c0.c1.s314" x[34] = 0.0; // - $"c0.c1.s324" x[35] = 0.0; // - $"c0.c1.s329" x[36] = 0.0; // - $"c0.c1.s330" x[37] = 0.0; // - $"c0.c1.s331" x[38] = 0.0; // - $"c0.c1.s332" x[39] = 0.0; // - $"c0.c1.s335" x[40] = 0.0; // - $"c0.c1.s338" x[41] = 0.059; // - $"c0.c1.s349" x[42] = 0.0; // - $"c0.c1.s350" x[43] = 0.7; // - $"c0.c1.s351" x[44] = 0.0; // - $"c0.c1.s352" x[45] = 0.0; // - $"c0.c1.s355" x[46] = 4.3; // - $"c0.c1.s358" x[47] = 0.6; // - $"c0.c1.s359" x[48] = 0.1; // - $"c0.c1.s360" x[49] = 0.0; // - $"c0.c1.s361" x[50] = 0.0; // - $"c0.c1.s362" x[51] = 0.0; // - $"c0.c1.s410" x[52] = 0.0; // - $"c0.c1.s421" x[53] = 0.57; // - $"c0.c1.s424" x[54] = 0.5; // - $"c0.c1.s430" x[55] = 0.1; // - $"c0.c1.s432" x[56] = 0.0; // - $"c0.c1.s435" x[57] = 0.0; // - $"c0.c1.s436" x[58] = 0.5; // - $"c0.c1.s437" x[59] = 0.0; // - $"c0.c1.s438" x[60] = 0.0; // - $"c0.c1.s439" x[61] = 0.0; // - $"c0.c1.s440" x[62] = 0.0; // - $"c0.c1.s441" x[63] = 0.5; // - $"c0.c1.s442" x[64] = 0.0; // - $"c0.c1.s443" x[65] = 0.0; // - $"c0.c1.s444" x[66] = 0.0; // - $"c0.c1.s446" x[67] = 0.0; // - $"c0.c1.s449" x[68] = 0.0; // - $"c0.c1.s456" x[69] = 0.0; // - $"c0.c1.s463" x[70] = 0.0; // - $"c0.c1.s467" x[71] = 0.0; // - $"c0.c1.s470" x[72] = 0.0; // - $"c0.c1.s477" x[73] = 0.0; // - $"c0.c1.s480" x[74] = 0.0; // - $"c0.c1.s487" x[75] = 0.0; // - $"c0.c1.s491" x[76] = 0.0; // - $"c0.c1.s496" x[77] = 0.0; // - $"c0.c1.s506" x[78] = 0.0; // - $"c0.c1.s512" x[79] = 0.0; // - $"c0.c1.s513" x[80] = 0.0; // - $"c0.c1.s520" x[81] = 0.0; // - $"c0.c1.s526" x[82] = 0.0; // - $"c0.c1.s539" x[83] = 0.0; // - $"c0.c1.s546" x[84] = 0.0; // - $"c0.c1.s55" x[85] = 0.0; // - $"c0.c1.s551" x[86] = 0.0; // - $"c0.c1.s564" x[87] = 0.0; // - $"c0.c1.s565" x[88] = 0.094; // - $"c0.c1.s566" x[89] = 0.0; // - $"c0.c1.s567" x[90] = 0.08; // - $"c0.c1.s568" x[91] = 0.15; // - $"c0.c1.s569" x[92] = 0.0; // - $"c0.c1.s57" x[93] = 0.4941; // - $"c0.c1.s570" x[94] = 0.2; // - $"c0.c1.s93" x[95] = 0.1; // - $"c0.c1.s98" x[96] = 0.0; // - $c0.s4 __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(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); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(time, x); } /* * calculate dy/dt for 'BIOMD0000000088.xml' model */ public void __internalDyDt_0(double time, double [] x, double[] result) { result[0] = -rate_re175-rate_re73+rate_re85*2; result[1] = -rate_re28+rate_re33; result[2] = -rate_re120-rate_re121+rate_re123+rate_re124-rate_re129+rate_re130-rate_re39; result[3] = -rate_re1; result[4] = -rate_re100*2-rate_re109+rate_re174+rate_re175-rate_re51-rate_re52+rate_re73-rate_re86-rate_re87-rate_re88-rate_re89-rate_re97; result[5] = +rate_re57+rate_re58-rate_re60-rate_re68*3; result[6] = -rate_re101+rate_re57+rate_re58-rate_re59-rate_re95; result[7] = +rate_re59; result[8] = +rate_re60; result[9] = -rate_re68; result[10] = +rate_re68; result[11] = +rate_re1-rate_re40; result[12] = +rate_re14+rate_re45; result[13] = +rate_re20-rate_re34; result[14] = +rate_re16-rate_re20-rate_re44-rate_re47-rate_re48; result[15] = +rate_re28-rate_re33; result[16] = +rate_re24-rate_re28+rate_re32-rate_re38-rate_re39; result[17] = -rate_re24-rate_re26+rate_re33+rate_re38; result[18] = +rate_re26-rate_re32; result[19] = -rate_re125-rate_re126+rate_re127+rate_re128-rate_re131+rate_re132+rate_re39; result[20] = -rate_re86; result[21] = +rate_re86-rate_re87-rate_re93; result[22] = +rate_re87-rate_re89-rate_re92; result[23] = -rate_re88+rate_re89-rate_re91; result[24] = +rate_re88-rate_re90; result[25] = -rate_re154-rate_re155+rate_re156+rate_re157-rate_re90-rate_re91-rate_re92-rate_re93; result[26] = -rate_re158-rate_re162+rate_re172+rate_re173+rate_re93; result[27] = -rate_re159-rate_re163+rate_re170+rate_re171+rate_re92; result[28] = -rate_re160-rate_re164+rate_re168+rate_re169+rate_re91; result[29] = -rate_re161-rate_re165+rate_re166+rate_re167+rate_re90; result[30] = -rate_re94-rate_re95-rate_re97; result[31] = -rate_re108-rate_re112+rate_re115+rate_re94; result[32] = +rate_re95; result[33] = -rate_re107-rate_re111+rate_re114+rate_re96; result[34] = +rate_re102-rate_re106-rate_re110+rate_re113; result[35] = +rate_re106; result[36] = +rate_re107; result[37] = +rate_re108; result[38] = +rate_re112-rate_re115; result[39] = +rate_re111-rate_re114; result[40] = +rate_re110-rate_re113; result[41] = -rate_re110-rate_re111-rate_re112+rate_re116-rate_re118; result[42] = +rate_re113+rate_re114+rate_re115-rate_re116-rate_re117; result[43] = -rate_re117-rate_re118-rate_re129-rate_re131-rate_re134-rate_re136+rate_re138+rate_re140+rate_re141; result[44] = +rate_re117-rate_re119; result[45] = +rate_re118+rate_re119; result[46] = -rate_re120-rate_re125+rate_re139+rate_re140-rate_re154-rate_re158-rate_re159-rate_re160-rate_re161; result[47] = -rate_re121+rate_re123-rate_re126+rate_re127-rate_re135-rate_re136+rate_re137+rate_re138-rate_re155+rate_re156-rate_re162-rate_re163-rate_re164-rate_re165+rate_re167+rate_re169+rate_re171+rate_re173; result[48] = +rate_re124+rate_re128-rate_re133-rate_re134+rate_re157+rate_re166+rate_re168+rate_re170+rate_re172; result[49] = +rate_re120-rate_re123; result[50] = +rate_re121-rate_re124; result[51] = +rate_re12-rate_re19; result[52] = +rate_re16-rate_re22; result[53] = -rate_re48-rate_re52; result[54] = -rate_re100+rate_re85; result[55] = -rate_re109+rate_re98; result[56] = -rate_re12+rate_re43; result[57] = +rate_re23-rate_re37; result[58] = +rate_re19-rate_re43; result[59] = +rate_re17-rate_re19+rate_re37; result[60] = +rate_re12-rate_re17-rate_re23; result[61] = -rate_re22+rate_re34+rate_re44+rate_re54; result[62] = +rate_re15-rate_re16; result[63] = -rate_re15+rate_re22; result[64] = +rate_re48-rate_re51; result[65] = +rate_re100-rate_re85; result[66] = +rate_re109-rate_re98; result[67] = +rate_re126-rate_re128; result[68] = +rate_re125-rate_re127; result[69] = +rate_re129-rate_re130; result[70] = +rate_re133-rate_re137; result[71] = +rate_re134-rate_re138; result[72] = +rate_re135-rate_re139; result[73] = +rate_re136-rate_re140; result[74] = +rate_re154-rate_re156; result[75] = +rate_re155-rate_re157; result[76] = +rate_re131-rate_re132; result[77] = +rate_re165-rate_re166; result[78] = +rate_re164-rate_re168; result[79] = +rate_re161-rate_re167; result[80] = +rate_re160-rate_re169; result[81] = +rate_re163-rate_re170; result[82] = +rate_re159-rate_re171; result[83] = +rate_re162-rate_re172; result[84] = +rate_re12-rate_re14+rate_re16; result[85] = +rate_re158-rate_re173; result[86] = +rate_re47+rate_re51-rate_re54-rate_re56+rate_re58; result[87] = +rate_re101-rate_re102; result[88] = -rate_re101-rate_re96+rate_re97; result[89] = +rate_re56-rate_re58; result[90] = +rate_re55-rate_re57; result[91] = -rate_re47+rate_re52+rate_re54-rate_re55+rate_re57; result[92] = -rate_re15+rate_re40-rate_re43-rate_re45; result[93] = +rate_re130+rate_re132-rate_re133-rate_re135+rate_re137+rate_re139-rate_re141; result[94] = -rate_re20+rate_re34; result[95] = -rate_re23-rate_re26+rate_re32+rate_re37; result[96] = +rate_re40; } protected double [] calculateResult(double time, double[] x) { double[] result = new double[97]; __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 ); } public double[] checkEvent(double time, double[] x) { this.time = time; __internalRateVarInitFunc_0(time, x); __internalRateVarInitFunc_1(time, x); __internalRateVarInitFunc_2(time, x); double [] flags = new double[1]; flags[0] = (time >= 300) ? +1 : -1; //event_0000001 return flags; } public void processEvent(int __internalVar12060040985150, double time, double[] x) { this.time = time; if ( __internalVar12060040985150 == 0) //event_0000001 { c0_s2 = 0.01; } } } // class ...