OneGeneInhibitoryNetwork.cpp Source File

00001 // OneGeneInhibitoryNetwork.cpp: implementation of the OneGeneInhibitoryNetwork class.
00002 //
00004 
00005 #ifdef _WINDOWS
00006 #include "stdafx.h"
00007 #endif
00008 
00009 #include "OneGeneInhibitoryNetwork.h"
00010 
00012 // Construction/Destruction
00014 
00015 OneGeneInhibitoryNetwork::OneGeneInhibitoryNetwork()
00016 {
00017         Chemical *freePromoter = new Chemical(chemicals.size(), 1.0, "P");
00018         chemicals.push_back(freePromoter);
00019 
00020         Chemical *boundPromoter = new Chemical(chemicals.size(), 0.0, "P:A");
00021         chemicals.push_back(boundPromoter);
00022 
00023         Chemical *mRNA = new Chemical(chemicals.size(), 0.0, "mRNA");
00024         chemicals.push_back(mRNA);
00025 
00026         Chemical *protein = new Chemical(chemicals.size(), 0.0, "A");
00027         chemicals.push_back(protein);
00028 
00029         RateConstant *kb = new RateConstant(0.6,0.2*0.6, "kb");
00030         rateConstants.push_back(kb);
00031         RateConstant *ku = new RateConstant(0.15,0.2*0.15, "ku");
00032         rateConstants.push_back(ku);
00033         RateConstant *ktm = new RateConstant(10.0,0.2*10.0, "ktm");
00034         rateConstants.push_back(ktm);
00035         RateConstant *kdm = new RateConstant(0.05,0.2*0.05, "kdm");
00036         rateConstants.push_back(kdm);
00037         RateConstant *kt = new RateConstant(1.2,0.2*1.2, "kt");
00038         rateConstants.push_back(kt);
00039         RateConstant *kd = new RateConstant(0.1,0.2*0.1, "kd");
00040         rateConstants.push_back(kd);
00041 
00042         PromoterBindingReaction *bindingReaction = new PromoterBindingReaction(freePromoter, protein, boundPromoter, kb, "tb");
00043         reactions.push_back(bindingReaction);
00044         PromoterUnbindingReaction *unbindingReaction = new PromoterUnbindingReaction(boundPromoter, freePromoter, protein, ku, "tu");
00045         reactions.push_back(unbindingReaction);
00046         TranscriptionReaction *transcriptionReaction = new TranscriptionReaction(freePromoter, mRNA, ktm, "tr");
00047         reactions.push_back(transcriptionReaction);
00048         RNADegradationReaction *mRNADegradationReaction = new RNADegradationReaction(mRNA, kdm, "tdm");
00049         reactions.push_back(mRNADegradationReaction);
00050         ProteinTranslationReaction *translationReaction = new ProteinTranslationReaction(mRNA, protein, kt, "tl");
00051         reactions.push_back(translationReaction);
00052         UnstableProteinDegradationReaction *proteinDegradationReaction = new UnstableProteinDegradationReaction(protein, kd, "tdA");
00053         reactions.push_back(proteinDegradationReaction);
00054 
00055 }
00056 
00057 OneGeneInhibitoryNetwork::~OneGeneInhibitoryNetwork()
00058 {
00059 
00060 }