AlternateOneGeneInhibitoryNetwork.cpp Source File

00001 // AlternateOneGeneInhibitoryNetwork.cpp: implementation of the CAlternateOneGeneInhibitoryNetwork class.
00002 //
00004 
00005 #include "AlternateOneGeneInhibitoryNetwork.h"
00006 
00008 // Construction/Destruction
00010 
00011 CAlternateOneGeneInhibitoryNetwork::CAlternateOneGeneInhibitoryNetwork()
00012 {
00013         Chemical *freePromoter = new Chemical(chemicals.size(), 1.0, "freePromoter");
00014         chemicals.push_back(freePromoter);
00015 
00016         Chemical *boundPromoter = new Chemical(chemicals.size(), 0.0, "boundPromoter");
00017         chemicals.push_back(boundPromoter);
00018 
00019         Chemical *mRNA = new Chemical(chemicals.size(), 0.0, "mRNA");
00020         chemicals.push_back(mRNA);
00021 
00022         Chemical *protein = new Chemical(chemicals.size(), 0.0, "protein");
00023         chemicals.push_back(protein);
00024 
00025         Chemical *zymogen = new Chemical(chemicals.size(), 0.0, "zymogen");
00026         chemicals.push_back(zymogen);
00027 
00028         RateConstant *kb = new RateConstant(0.6, "kb");
00029         rateConstants.push_back(kb);
00030         RateConstant *ku = new RateConstant(0.15, "ku");
00031         rateConstants.push_back(ku);
00032         RateConstant *ktm = new RateConstant(10.0, "ktm");
00033         rateConstants.push_back(ktm);
00034         RateConstant *kdm = new RateConstant(0.05, "kdm");
00035         rateConstants.push_back(kdm);
00036         RateConstant *kt = new RateConstant(1.0, "kt");
00037         rateConstants.push_back(kt);
00038         RateConstant *kd = new RateConstant(0.1, "kd");
00039         rateConstants.push_back(kd);
00040         RateConstant *ktz = new RateConstant(15.0, "ktz");
00041         rateConstants.push_back(ktz);
00042         RateConstant *kdz = new RateConstant(0.02,"kdz");
00043         rateConstants.push_back(kdz);
00044         RateConstant *kpro = new RateConstant(0.05,"kpro");
00045         rateConstants.push_back(kpro);
00046 
00047 
00048         PromoterBindingReaction *bindingReaction = new PromoterBindingReaction(freePromoter, protein, boundPromoter, kb, "bindingReaction");
00049         reactions.push_back(bindingReaction);
00050         PromoterUnbindingReaction *unbindingReaction = new PromoterUnbindingReaction(boundPromoter, freePromoter, protein, ku, "unbindingReaction");
00051         reactions.push_back(unbindingReaction);
00052         TranscriptionReaction *transcriptionReaction = new TranscriptionReaction(freePromoter, mRNA, ktm, "transcriptionReaction");
00053         reactions.push_back(transcriptionReaction);
00054         RNADegradationReaction *mRNADegradationReaction = new RNADegradationReaction(mRNA, kdm, "mRNADegradationReaction");
00055         reactions.push_back(mRNADegradationReaction);
00056         ProteinTranslationReaction *translationReaction = new ProteinTranslationReaction(mRNA, protein, kt, "translationReaction");
00057         reactions.push_back(translationReaction);
00058         UnstableProteinDegradationReaction *proteinDegradationReaction = new UnstableProteinDegradationReaction(protein, kd, "proteinDegradationReaction");
00059         reactions.push_back(proteinDegradationReaction);
00060         ProteinTranslationReaction *zymogenTranslation = new ProteinTranslationReaction(mRNA, zymogen, ktz, "zymogenTranslation");
00061         reactions.push_back(zymogenTranslation);
00062         UnstableProteinDegradationReaction *zymogenDegradationReaction = new UnstableProteinDegradationReaction(zymogen, kdz, "zymogenDegradationReaction");
00063         reactions.push_back(zymogenDegradationReaction);
00064         TransformationReaction *proteolyticCleavage = new TransformationReaction(zymogen, protein, kpro, "proteolyticCleavage");
00065         reactions.push_back(proteolyticCleavage);
00066 
00067 }
00068 
00069 CAlternateOneGeneInhibitoryNetwork::~CAlternateOneGeneInhibitoryNetwork()
00070 {
00071 
00072 }