LaubLoomisDictyNetwork.cpp Source File

00001 // LaubLoomisDictyNetwork.cpp: implementation of the CLaubLoomisDictyNetwork class.
00002 //
00004 
00005 #include "LaubLoomisDictyNetwork.h"
00006 
00008 // Construction/Destruction
00010 
00011 CLaubLoomisDictyNetwork::CLaubLoomisDictyNetwork()
00012 {
00013         // #molecules/uM
00014         double CFactor = 300000; 
00015         double SecPerMin = 60.0;
00016 
00017         // chemical species
00018         Chemical *ACA = new Chemical(chemicals.size(),1.0*CFactor,"ACA");
00019         chemicals.push_back(ACA);
00020 
00021         Chemical *PKA = new Chemical(chemicals.size(),1.0*CFactor,"PKA");
00022         chemicals.push_back(PKA);
00023 
00024         Chemical *ERK2 = new Chemical(chemicals.size(),1.5*CFactor,"ERK2");
00025         chemicals.push_back(ERK2);
00026 
00027         Chemical *REGA = new Chemical(chemicals.size(),2.5*CFactor,"REGA");
00028         chemicals.push_back(REGA);
00029 
00030         Chemical *cAMPi = new Chemical(chemicals.size(),1.0*CFactor,"cAMPi");
00031         chemicals.push_back(cAMPi);
00032 
00033         Chemical *cAMPe = new Chemical(chemicals.size(),0.1*CFactor,"cAMPe");
00034         chemicals.push_back(cAMPe);
00035 
00036         Chemical *CAR1 = new Chemical(chemicals.size(),1.5*CFactor,"CAR1");
00037         chemicals.push_back(CAR1);
00038 
00039         // rate constants
00040         RateConstant *k1 = new RateConstant(2.0,"k1");
00041         rateConstants.push_back(k1);
00042 
00043         RateConstant *k2 = new RateConstant(0.9/CFactor,"k2");
00044         rateConstants.push_back(k2);
00045 
00046         RateConstant *k3 = new RateConstant(2.5,"k3");
00047         rateConstants.push_back(k3);
00048 
00049         RateConstant *k4 = new RateConstant(1.5,"k4");
00050         rateConstants.push_back(k4);
00051 
00052         RateConstant *k5 = new RateConstant(0.6,"k5");
00053         rateConstants.push_back(k5);
00054 
00055         RateConstant *k6 = new RateConstant(0.8/CFactor,"k6");
00056         rateConstants.push_back(k6);
00057 
00058         RateConstant *k7 = new RateConstant(1.0*CFactor,"k7");
00059         rateConstants.push_back(k7);
00060 
00061         RateConstant *k8 = new RateConstant(1.3/CFactor,"k8");
00062         rateConstants.push_back(k8);
00063 
00064         RateConstant *k9 = new RateConstant(0.3,"k9");
00065         rateConstants.push_back(k9);
00066 
00067         RateConstant *k10 = new RateConstant(0.8/CFactor,"k10");
00068         rateConstants.push_back(k10);
00069 
00070         RateConstant *k11 = new RateConstant(0.7,"k11");
00071         rateConstants.push_back(k11);
00072 
00073         RateConstant *k12 = new RateConstant(4.9,"k12");
00074         rateConstants.push_back(k12);
00075 
00076         RateConstant *k13 = new RateConstant(23.0,"k13");
00077         rateConstants.push_back(k13);
00078 
00079         RateConstant *k14 = new RateConstant(4.5,"k14");
00080         rateConstants.push_back(k14);
00081 
00082         // reactions
00083 
00084         Reaction *ACACreation = new GenerationReaction(CAR1,ACA,k1,"ACACreation");
00085         reactions.push_back(ACACreation);
00086 
00087         Reaction *ACADestruction = new CFirstOrderDestructionReaction(PKA,ACA,k2,"ACADestruction");
00088         reactions.push_back(ACADestruction);
00089 
00090         Reaction *PKACreation = new GenerationReaction(cAMPi,PKA,k3,"PKACreation");
00091         reactions.push_back(PKACreation);
00092 
00093         Reaction *PKADegradation = new UnstableProteinDegradationReaction(PKA,k4,"PKADegradation");
00094         reactions.push_back(PKADegradation);
00095 
00096         Reaction *ERK2Creation = new GenerationReaction(CAR1,ERK2,k5,"ERK2Creation");
00097         reactions.push_back(ERK2Creation);
00098 
00099         Reaction *ERK2Destruction = new CFirstOrderDestructionReaction(PKA,ERK2,k6,"ERK2Destruction");
00100         reactions.push_back(ERK2Destruction);
00101 
00102         Reaction *REGACreation = new CConstantSourceReaction(REGA,k7,"REGACreation");
00103         reactions.push_back(REGACreation);
00104 
00105         Reaction *REGADestruction = new CFirstOrderDestructionReaction(ERK2,REGA,k8,"REGADestruction");
00106         reactions.push_back(REGADestruction);
00107 
00108         Reaction *cAMPiCreation = new GenerationReaction(ACA,cAMPi,k9,"cAMPiCreation");
00109         reactions.push_back(cAMPiCreation);
00110 
00111         Reaction *cAMPiDestruction = new CFirstOrderDestructionReaction(REGA,cAMPi,k10,"cAMPiDestruction");
00112         reactions.push_back(cAMPiDestruction);
00113 
00114         Reaction *cAMPeCreation = new GenerationReaction(ACA,cAMPe,k11,"cAMPeCreation");
00115         reactions.push_back(cAMPeCreation);
00116 
00117         Reaction *cAMPeDestruction = new UnstableProteinDegradationReaction(cAMPe,k12,"cAMPeDegradation");
00118         reactions.push_back(cAMPeDestruction);
00119 
00120         Reaction *CAR1Creation = new GenerationReaction(cAMPe,CAR1,k13,"CAR1Creation");
00121         reactions.push_back(CAR1Creation);
00122 
00123         Reaction *CAR1Degradation = new UnstableProteinDegradationReaction(CAR1,k14,"CAR1Degradation");
00124         reactions.push_back(CAR1Degradation);
00125 }
00126 
00127 CLaubLoomisDictyNetwork::~CLaubLoomisDictyNetwork()
00128 {
00129 
00130 }