fillOrphanMetabolites <- function(reference, reactionList, limit, reference_metabolites, oM, newR) {
repeat({
aC <- additionCost(reactionList = reference, reference = reactionList)
rA <- reference[aC <= limit]
whichAdd <- unlist(lapply(reference_metabolites[aC <= limit], function(sR) {
any(sR %in% oM)
}))
toAdd <- rA[whichAdd]
aC <- aC[aC <= limit][whichAdd]
if (any(!toAdd %in% newR$react)) {
newR <- rbind(newR, data.frame("addCost" = aC, "react" = toAdd))
newR <- newR[!duplicated(newR$react), ]
reactionList <- unique(c(reactionList, newR$react))
} else {
break()
}
})
return(list("new" = newR, "summary" = reactionList))
}
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