MartielGoldbeterDictyNetwork.cpp Source File

00001 // MartielGoldbeterDictyNetwork.cpp: implementation of the CMartielGoldbeterDictyNetwork class.
00002 //
00004 
00005 #include "MartielGoldbeterDictyNetwork.h"
00006 
00008 // Construction/Destruction
00010 
00011 CMartielGoldbeterDictyNetwork::CMartielGoldbeterDictyNetwork()
00012 {
00013         // #molecules/uM
00014         double CFactor = 300000;
00015         double SecPerMin = 60.0;
00016 
00017         // chemical species
00018         Chemical *R = new Chemical(chemicals.size(),1.0*CFactor,"R");
00019         chemicals.push_back(R);
00020 
00021         Chemical *D = new Chemical(chemicals.size(),0.0,"D");
00022         chemicals.push_back(D);
00023 
00024         Chemical *BoundR = new Chemical(chemicals.size(),0.0,"BoundR");
00025         chemicals.push_back(BoundR);
00026 
00027         Chemical *BoundD = new Chemical(chemicals.size(),0.0,"BoundD");
00028         chemicals.push_back(BoundD);
00029 
00030         Chemical *E = new Chemical(chemicals.size(),0.0,"E");
00031         chemicals.push_back(E);
00032 
00033         Chemical *C = new Chemical(chemicals.size(),(1.0/15.0)*CFactor,"C");
00034         chemicals.push_back(C);
00035 
00036         Chemical *cAMPi = new Chemical(chemicals.size(),0.0,"cAMPi");
00037         chemicals.push_back(cAMPi);
00038 
00039         Chemical *cAMPe = new Chemical(chemicals.size(),0.0,"cAMPe");
00040         chemicals.push_back(cAMPe);
00041 
00042         // rate constants
00043         RateConstant *kp1 = new RateConstant(0.036,"kp1");
00044         rateConstants.push_back(kp1);
00045 
00046         RateConstant *km1 = new RateConstant(0.36,"km1");
00047         rateConstants.push_back(km1);
00048 
00049         RateConstant *kp2 = new RateConstant(0.666,"kp2");
00050         rateConstants.push_back(kp2);
00051 
00052         RateConstant *km2 = new RateConstant(0.00333,"km2");
00053         rateConstants.push_back(km2);
00054 
00055         RateConstant *a1 = new RateConstant(1.0,"a1");
00056         rateConstants.push_back(a1);
00057 
00058         RateConstant *d1 = new RateConstant(30000,"d1");
00059         rateConstants.push_back(d1);
00060 
00061         RateConstant *a2 = new RateConstant(1.0,"a2");
00062         rateConstants.push_back(a2);
00063 
00064         RateConstant *d2 = new RateConstant(3000,"d2");
00065         rateConstants.push_back(d2);
00066 
00067         RateConstant *a3 = new RateConstant(1.0,"a3");
00068         rateConstants.push_back(a3);
00069 
00070         RateConstant *d3 = new RateConstant(30000,"d3");
00071         rateConstants.push_back(d3);
00072 
00073         RateConstant *k4 = new RateConstant(1.0,"k4");
00074         rateConstants.push_back(k4);
00075 
00076         RateConstant *k5 = new RateConstant(10.0,"k5");
00077         rateConstants.push_back(k5);
00078 
00079         RateConstant *ki = new RateConstant(1.7,"ki");
00080         rateConstants.push_back(ki);
00081 
00082         RateConstant *kt = new RateConstant(0.9,"kt");
00083         rateConstants.push_back(kt);
00084 
00085         RateConstant *ke = new RateConstant(5.4,"ke");
00086         rateConstants.push_back(ke);
00087 
00088         // reactions
00089         Reaction *FreeDesensitization = new TransformationReaction(R,D,kp1,"FreeDesensitization");
00090         reactions.push_back(FreeDesensitization);
00091 
00092         Reaction *FreeResensitization = new TransformationReaction(D,R,km1,"FreeResensitization");
00093         reactions.push_back(FreeResensitization);
00094 
00095         Reaction *RBindingcAMP = new HeterodimerizationReaction(R,cAMPe,BoundR,a1,"RBindingcAMP");
00096         reactions.push_back(RBindingcAMP);
00097 
00098         Reaction *RUnbindingcAMP = new HeterodimerDissociationReaction(BoundR,R,cAMPe,d1,"RUnbindingcAMP");
00099         reactions.push_back(RUnbindingcAMP);
00100 
00101         Reaction *DBindingcAMP = new HeterodimerizationReaction(D,cAMPe,BoundD,a2,"DBindingcAMP");
00102         reactions.push_back(DBindingcAMP);
00103 
00104         Reaction *DUnbindingcAMP = new HeterodimerDissociationReaction(BoundD,D,cAMPe,d2,"DUnbindingcAMP");
00105         reactions.push_back(DUnbindingcAMP);
00106 
00107         Reaction *BoundDesensitization = new TransformationReaction(BoundR,BoundD,kp2,"BoundDesensitization");
00108         reactions.push_back(BoundDesensitization);
00109 
00110         Reaction *BoundResensitization = new TransformationReaction(BoundD,BoundR,km2,"BoundResensitization");
00111         reactions.push_back(BoundResensitization);
00112 
00113         Reaction *ComplexFormation = new CTrimerFormation(BoundR,BoundR,C,E,a3,"ComplexFormation");
00114         reactions.push_back(ComplexFormation);
00115 
00116         Reaction *ComplexDissociation = new CTrimerDissociation(E,BoundR,BoundR,C,d3,"ComplexDissociation");
00117         reactions.push_back(ComplexDissociation);
00118 
00119         Reaction *ComplexcAMPProduction = new GenerationReaction(E,cAMPi,k4,"ComplexcAMPProduction");
00120         reactions.push_back(ComplexcAMPProduction);
00121 
00122         Reaction *CyclasecAMPProduction = new GenerationReaction(C,cAMPi,k5,"CyclasecAMPProduction");
00123         reactions.push_back(CyclasecAMPProduction);
00124 
00125         Reaction *InternalHydrolysis = new UnstableProteinDegradationReaction(cAMPi,ki,"InternalHydrolysis");
00126         reactions.push_back(InternalHydrolysis);
00127 
00128         Reaction *cAMPTransport = new ChemicalTransportReaction(cAMPi,cAMPe,kt,"cAMPTransport");
00129         reactions.push_back(cAMPTransport);
00130 
00131         Reaction *ExternalHydrolysis = new UnstableProteinDegradationReaction(cAMPe,ke,"ExternalHydrolysis");
00132         reactions.push_back(ExternalHydrolysis);
00133 }
00134 
00135 CMartielGoldbeterDictyNetwork::~CMartielGoldbeterDictyNetwork()
00136 {
00137 
00138 }