Open the enzyme builder functions

docs/src/examples/05-enzyme-constrained-models.jl

@@ -138,13 +138,20 @@ m.enzymes.b2417.bound = C.Between(0.0, 0.1) # for fun, change the bounds of the
 # attach the enzyme mass balances
 m = add_enzyme_constraints!(
     m,
-    reaction_isozymes,
-    gene_molar_masses,
-    [("total_proteome_bound", A.genes(model), total_enzyme_capacity)];
+    reaction_isozymes;
     fluxes = m.fluxes, # mount enzyme constraints to these fluxes
     enzymes = m.enzymes, # enzyme variables
 )
 
+# add capacity limitation
+m *=
+    :total_proteome_bound^enzyme_capacity(
+        m.enzymes,
+        gene_molar_masses,
+        A.genes(model),
+        total_enzyme_capacity,
+    )
+
 # solve the model
 ec_solution = optimized_constraints(
     m;

src/builders/enzymes.jl

@@ -127,22 +127,37 @@ end
 """
 $(TYPEDSIGNATURES)
 
-Create enzyme capacity limitation.
+Create a enzyme capacity limitation. Bounds the gene product masses (concentration
+* molar mass) of gene products in `enzyme_ids` by `capacity_bound`.
 """
 function enzyme_capacity(
     enzymes::C.ConstraintTree,
     gene_molar_masses::Dict{String,Float64},
     enzyme_ids::Vector{String},
-    capacity::Float64,
+    capacity_bound::C.Bound,
 )
     C.Constraint(
         value = sum(
             enzymes[Symbol(gid)].value * gene_molar_masses[gid] for gid in enzyme_ids
         ),
-        bound = C.Between(0.0, capacity),
+        bound = capacity_bound,
     )
 end
 
+"""
+$(TYPEDSIGNATURES)
+
+Create an enzyme capacity limitation. Bounds the gene product masses
+(concentration * molar mass) of gene products in `enzyme_ids` between `[0, capacity]`.
+"""
+enzyme_capacity(
+    enzymes::C.ConstraintTree,
+    gene_molar_masses::Dict{String,Float64},
+    enzyme_ids::Vector{String},
+    capacity::Float64,
+) = enzyme_capacity(enzymes, gene_molar_masses, enzyme_ids, C.Between(0.0, capacity))
+
+
 export enzyme_capacity
 
 """
@@ -164,9 +179,7 @@ assign kcats to reactions. Use [`SimpleIsozyme`](@ref) when in doubt.
 """
 function add_enzyme_constraints!(
     m::C.ConstraintTree,
-    reaction_isozymes::Dict{String,Dict{String,T}},
-    gene_molar_masses::Dict{String,Float64},
-    capacity_limitations::Vector{Tuple{String,Vector{String},Float64}};
+    reaction_isozymes::Dict{String,Dict{String,T}};
     fluxes = m.fluxes,
     enzymes = m.enzymes,
 ) where {T<:Isozyme}
@@ -225,11 +238,6 @@ function add_enzyme_constraints!(
             reaction_isozymes,
         )
 
-    # add capacity limitations
-    for (id, gids, cap) in capacity_limitations
-        m *= Symbol(id)^enzyme_capacity(enzymes, gene_molar_masses, gids, cap)
-    end
-
     m
 end
 

src/frontend/enzyme_constrained_flux_balance_analysis.jl

@@ -29,12 +29,13 @@ function enzyme_constrained_flux_balance_analysis(
     # create enzyme variables
     m += :enzymes^enzyme_variables(model)
 
-    m = add_enzyme_constraints!(
-        m,
-        reaction_isozymes,
-        gene_molar_masses,
-        capacity_limitations,
-    )
+    # add enzyme equality constraints (stoichiometry)
+    m = add_enzyme_constraints!(m, reaction_isozymes)
+
+    # add capacity limitations
+    for (id, gids, cap) in capacity_limitations
+        m *= Symbol(id)^enzyme_capacity(m.enzymes, gene_molar_masses, gids, cap)
+    end
 
     for rid in Symbol.(unconstrain_reactions)
         m.fluxes[rid].bound = C.Between(-1000.0, 1000.0)

test/runtests.jl

@@ -45,7 +45,6 @@ run_test_file("data_downloaded.jl")
 
 @testset "COBREXA test suite" begin
     run_doc_examples()
-    include("enzyme_model.jl")
     run_test_file("aqua.jl")
 end