Delete initData.R

networkComplexityBigg/envirDist/initData.R

-initData <- function(){
-	uptakeLowBnd <- -10
-	bioThreshold <- 1e-2
-	#bioThreshold <- 10
-	
-	print(load("~/DATA/universalBiGG.ver2.Rdata"))
-	uni <- uni2
-
-	print(load("~/DATA/mediaBiGGwithRandom.Rdata"))
-modelReactMap[["iIS312"]]=append(modelReactMap[["iIS312"]],c("UMPK_B", "ADKd", "DADNt2_LR", "DGSNt2_LR","NTD8_B", 
-                                                             "TYRabc", "TRPabc", "AMPt6", "CMPt6", "DTMPt6", "DURIK1_1"
-	                                                             ,"DURIt2_B", "MANpts_B" ))
-modelReactMap[["iIS312_Amastigote"]]=append(modelReactMap[["iIS312_Amastigote"]],c("DADK_B", "DGSNt","DTTPt","DCTPD2","DADNt2_LR",
-                                                                        "TYRabc","TRPabc", "MAN6Pt6_2", "AMPt6","ADADir_LR",
-                                                             "CMPt6","DCYTt2_B","DGNSK_1"  ))	
-	modelReactMap[["iIS312_Epimastigote"]]=append(modelReactMap[["iIS312_Epimastigote"]],c("UMPK_B", "ADKd","DTTPt","DGSNt2_LR",
-	"NTD8_B","TYRabc","TRPabc","ADADir_B","AMPt6","CMPt6", "MAN1Pt6","DADNt2_B","DCYTt2_B"))	
-	modelReactMap[["iIS312_Trypomastigote"]]=append(modelReactMap[["iIS312_Trypomastigote"]],c("ADKd","UMPK_copy2_LR",
-	"DGSNt2_LR","TYRabc","TRPabc","F6Pt6_2","AMPt6","CMPt6","DTMPt6","DADNt2_B","DGNSK_1","DURIK1_1","DURIt2_B"))
-	modelReactMap[["iLJ478"]]=append(modelReactMap[["iLJ478"]],"ASNt2r_LR")
-modelReactMap[["iSM199"]]=append(modelReactMap[["iSM199"]],c("LEUTAi","ILEabc","VALt2r_LR","ILETA2_LR","PHEabc"))
-	
-	ex <- findExchReact(uni)
-	exOnly <- ex[grep("^EX_", react_id(ex))]
-	exMap <- react_pos(exOnly)
-	names(exMap) <- gsub("\\[\\w\\]$", "", met_id(exOnly))
-	
-	# setting media constraints
-	mediaLowBounds <- lapply(mediaBiGG, function(m){
-		lb <- lowbnd(uni)
-		lb[exMap] <- 0
-		lb[exMap[names(exMap) %in% m]] <- uptakeLowBnd
-		return(lb)
-	})
-
-	modelReactMapById <- lapply(modelReactMap, function(x){
-		union(match(x, react_id(uni)), exMap)# this little fucker... adding all exchange reactions to the models.
-	})
-
-	modelBiomassMapSelectionById <- match(modelBiomassMapSelection, react_id(uni))
-	names(modelBiomassMapSelectionById) <- names(modelBiomassMapSelection)
-	
-	modelRmEnergyCyclesById <- lapply(modelRmEnergyCycles, function(x){
-		lapply(x, function(y) match(y, react_id(uni)))
-	})
-	
-	for(i in ls()) assign(x=i, value=get(i), envir=.GlobalEnv)
-	return(T)
-}
-