R/BiGGR-internal.R

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

##Get a subset of a model in which all reactions, species, compartments are associated
##  with the reactions in argument reaction.ids (a list or vector of character objects).
##  Returns a rsbml Model object. This is an internal function 
.buildSubModel <- function(model, reaction.ids){
##Get all reactions
relevant.reactions <- model@reactions[reaction.ids]
##Get all species that are associated with given reactions
relevant.species.names <- unique(unlist(sapply(relevant.reactions, function(r){
lapply(c(r@reactants, r@products), function(sr){
  model@species[[sr@species]]@id
})
})))
##remove duplicates
relevant.species <- model@species[relevant.species.names]
##Get the compartments from the species
relevant.compartment.names <- unique(sapply(relevant.species, function(s)s@compartment))
relevant.compartments <- model@compartments[relevant.compartment.names]

##Build SBML model from reactions, species and compartments
new("Model", species=relevant.species, reactions=relevant.reactions, compartments=relevant.compartments)
}