Merge pull request #530 from LCSB-BioCore/mo-change-objective

added `change_objective!` function and tests

src/reconstruction/CoreModel.jl

@@ -436,3 +436,39 @@ end
 @_remove_fn metabolite CoreModel String plural begin
     remove_metabolites(model, Int.(indexin(metabolite_ids, metabolites(model))))
 end
+
+"""
+    change_objective!(
+        model::CoreModel,
+        rxn_idxs::Vector{Int};
+        weights = ones(length(rxn_idxs)),
+    )
+
+Change the objective for `model` to reaction(s) with indices `rxn_idxs`, optionally
+specifying their `weights`. By default, assume equal weights. If no objective exists in
+model, sets objective. Note, also accepts `String` or `Vector{String}` of reaction ids.
+"""
+function change_objective!(
+    model::CoreModel,
+    rxn_idxs::Vector{Int};
+    weights = ones(length(rxn_idxs)),
+)
+    model.c = spzeros(length(model.c))
+    model.c[rxn_idxs] .= weights
+    nothing
+end
+
+change_objective!(model::CoreModel, rxn_idx::Int) = change_objective!(model, [rxn_idx])
+
+function change_objective!(
+    model::CoreModel,
+    rxn_ids::Vector{String};
+    weights = ones(length(rxn_ids)),
+)
+    idxs = indexin(rxn_ids, reactions(model))
+    any(isnothing(idx) for idx in idxs) &&
+        throw(DomainError(rxn_ids, "Some reaction ids were not found in model."))
+    change_objective!(model, Int.(idxs); weights)
+end
+
+change_objective!(model::CoreModel, rxn_id::String) = change_objective!(model, [rxn_id])

src/reconstruction/CoreModelCoupled.jl

@@ -424,3 +424,26 @@ end
 @_remove_fn metabolite CoreModelCoupled String plural begin
     remove_metabolites(model, Int.(indexin(metabolite_ids, metabolites(model))))
 end
+
+"""
+    change_objective!(
+        model::CoreModelCoupled,
+        args...,
+        kwargs...,
+    )
+
+Forwards arguments to [`change_objective!`](@ref).
+"""
+function change_objective!(model::CoreModelCoupled, args...; kwargs...)
+    change_objective!(model.lm, args...; kwargs...)
+end
+
+change_objective!(model::CoreModelCoupled, rxn_xid::Int) =
+    change_objective!(model.lm, [rxn_xid])
+
+function change_objective!(model::CoreModelCoupled, args...; kwargs...)
+    change_objective!(model.lm, args...; kwargs...)
+end
+
+change_objective!(model::CoreModelCoupled, rxn_id::String) =
+    change_objective!(model, [rxn_id])

src/reconstruction/StandardModel.jl

@@ -230,3 +230,31 @@ end
     remove_metabolites!(n, metabolite_ids)
     return n
 end
+
+"""
+    change_objective!(
+        model::StandardModel,
+        rxn_ids::Vector{String};
+        weights = ones(length(rxn_ids)),
+    )
+
+Change the objective for `model` to reaction(s) with `rxn_ids`, optionally specifying their `weights`. By default,
+assume equal weights. If no objective exists in model, sets objective.
+"""
+function change_objective!(
+    model::StandardModel,
+    rxn_ids::Vector{String};
+    weights = ones(length(rxn_ids)),
+)
+    all(!haskey(model.reactions, rid) for rid in rxn_ids) &&
+        throw(DomainError(rxn_ids, "Some reaction ids were not found in model."))
+
+    for (_, rxn) in model.reactions # reset to zero
+        rxn.objective_coefficient = 0.0
+    end
+    for (k, rid) in enumerate(rxn_ids)
+        model.reactions[rid].objective_coefficient = weights[k]
+    end
+end
+
+change_objective!(model::StandardModel, rxn_id::String) = change_objective!(model, [rxn_id])

test/reconstruction/CoreModel.jl

@@ -248,4 +248,8 @@ end
     add_reactions!(toymodel, [rxn2, rxn3])
     @test size(toymodel.S) == (6, 10)
     @test toymodel.xl[end] == 10
+
+    change_objective!(toymodel, "nr1")
+    @test objective(toymodel)[8] == 1.0
+    @test objective(toymodel)[7] == 0.0
 end

test/reconstruction/StandardModel.jl

@@ -109,4 +109,8 @@
 
     remove_gene!(model, "g1")
     @test length(model.genes) == 4
+
+    ### objective
+    change_objective!(model, "r2")
+    @test model.reactions["r2"].objective_coefficient == 1.0
 end