rename kwarg to be even more consistent

docs/src/examples/14_simplified_enzyme_constrained.jl

@@ -63,7 +63,7 @@ simplified_enzyme_constrained_model =
     model |> with_simplified_enzyme_constraints(
         reaction_isozyme = rxn_isozymes,
         gene_product_molar_mass = gene_product_masses,
-        total_enzyme_capacity = 50.0,
+        total_gene_product_mass_bound = 50.0,
     )
 
 # (You could alternatively use the [`make_simplified_enzyme_constrained_model`](@ref) to create the

src/reconstruction/enzyme_constrained.jl

@@ -1,15 +1,20 @@
 """
 $(TYPEDSIGNATURES)
 
-Wrap a model into a [`EnzymeConstrainedModel`](@ref), following the structure
-given by GECKO algorithm (see [`EnzymeConstrainedModel`](@ref) documentation for
-details). Multiple capacity constraints can be placed on the model using the
+Wrap a model into an [`EnzymeConstrainedModel`](@ref), following the structure
+given by the GECKO algorithm (see [`EnzymeConstrainedModel`](@ref) documentation
+for details). Multiple capacity constraints can be placed on the model using the
 kwargs.
 
-Parameters `gene_product_mass_group` and `gene_product_mass_group_bound` specify the groups of gene products and the respective total limit of total mass of the gene products for each group. Gene products not listed in any gene product mass group are ignored.
+Parameters `gene_product_mass_group` and `gene_product_mass_group_bound` specify
+the groups of gene products and the respective total capacity limit of the gene
+products for each group. Gene products not listed in any gene product mass group
+are ignored.
 
-For simplicity in many use cases, specifying the `total_enzyme_capacity` argument overrides the above arguments by specifying a single group called `uncategorized` of all gene products, with the corresponding mass bound.
-- `gene_product_mass_group` is a dict that returns a vector of gene IDs
+For simplicity, in many use cases specifying the `total_gene_product_mass_bound`
+argument overrides the above arguments by specifying a single group called
+`uncategorized` of all gene products, with the corresponding mass capacity
+bound.
 
 # Example
 ```
@@ -27,26 +32,31 @@ ecmodel = make_enzyme_constrained_model(
 
 ecmodel2 = make_enzyme_constrained_model(
     model;
-    total_enzyme_capacity = 0.5
-) 
+    total_gene_product_mass_bound = 0.5
+)
 ```
 # Notes
 Reactions with no turnover number data, or non-enzymatic reactions that should
 be ignored, *must* have `nothing` in the `gene_associations` field of the
 associated reaction.
+
+The capacity bound
 """
 function make_enzyme_constrained_model(
     model::AbstractMetabolicModel;
     gene_product_mass_group::Maybe{Dict{String,Vector{String}}} = nothing,
     gene_product_mass_group_bound::Maybe{Dict{String,Float64}} = nothing,
-    total_enzyme_capacity::Maybe{Float64} = nothing,
+    total_gene_product_mass_bound::Maybe{Float64} = nothing,
 )
-    if !isnothing(total_enzyme_capacity)
+    if !isnothing(total_gene_product_mass_bound)
         gene_product_mass_group = Dict("uncategorized" => genes(model))
-        gene_product_mass_group_bound = Dict("uncategorized" => total_enzyme_capacity)
+        gene_product_mass_group_bound =
+            Dict("uncategorized" => total_gene_product_mass_bound)
     end
-    isnothing(gene_product_mass_group) && throw(ArgumentError("missing mass group specification"))
-    isnothing(gene_product_mass_group_bound) && throw(ArgumentError("missing mass group bounds"))
+    isnothing(gene_product_mass_group) &&
+        throw(ArgumentError("missing mass group specification"))
+    isnothing(gene_product_mass_group_bound) &&
+        throw(ArgumentError("missing mass group bounds"))
 
     gpb_(gid) = (gene_product_lower_bound(model, gid), gene_product_upper_bound(model, gid))
 

src/reconstruction/simplified_enzyme_constrained.jl

@@ -7,7 +7,7 @@ Construct a model with a structure given by sMOMENT algorithm; returns a
 # Arguments
 - a `model` that implements the accessors `gene_product_molar_mass`,
   `reaction_isozymes`.
-- `total_enzyme_capacity` is the maximum "enzyme capacity" in the model.
+- `total_gene_product_mass_bound` is the maximum "enzyme capacity" in the model.
 
 # Notes
 The SMOMENT algorithm only uses one [`Isozyme`](@ref) per reaction. If multiple
@@ -20,7 +20,7 @@ associated reaction.
 """
 function make_simplified_enzyme_constrained_model(
     model::AbstractMetabolicModel;
-    total_enzyme_capacity::Float64 = 0.5,
+    total_gene_product_mass_bound::Float64 = 0.5,
 )
     # helper function to rank the isozymes by relative speed
     speed_enzyme(model, isozyme) =
@@ -88,5 +88,5 @@ function make_simplified_enzyme_constrained_model(
         end
     end
 
-    return SimplifiedEnzymeConstrainedModel(columns, total_enzyme_capacity, model)
+    return SimplifiedEnzymeConstrainedModel(columns, total_gene_product_mass_bound, model)
 end

src/types/wrappers/SimplifiedEnzymeConstrainedModel.jl

@@ -45,7 +45,7 @@ is retained.
 
 In the structure, the field `columns` describes the correspondence of
 stoichiometry columns to the stoichiometry and data of the internal wrapped
-model, and `total_enzyme_capacity` is the total bound on the enzyme capacity
+model, and `total_gene_product_mass_bound` is the total bound on the enzyme capacity
 consumption as specified in sMOMENT algorithm.
 
 This implementation allows easy access to fluxes from the split reactions
@@ -59,7 +59,7 @@ $(TYPEDFIELDS)
 """
 struct SimplifiedEnzymeConstrainedModel <: AbstractModelWrapper
     columns::Vector{_SimplifiedEnzymeConstrainedColumn}
-    total_enzyme_capacity::Float64
+    total_gene_product_mass_bound::Float64
 
     inner::AbstractMetabolicModel
 end
@@ -122,5 +122,5 @@ Accessors.n_coupling_constraints(model::SimplifiedEnzymeConstrainedModel) =
 
 Accessors.coupling_bounds(model::SimplifiedEnzymeConstrainedModel) =
     let (iclb, icub) = coupling_bounds(model.inner)
-        (vcat(iclb, [0.0]), vcat(icub, [model.total_enzyme_capacity]))
+        (vcat(iclb, [0.0]), vcat(icub, [model.total_gene_product_mass_bound]))
     end

test/reconstruction/constrained_allocation.jl

@@ -57,7 +57,10 @@
     @test first(m.reactions["r6"].gene_associations).kcat_forward == 10.0
 
 
-    cam = make_simplified_enzyme_constrained_model(ribomodel; total_enzyme_capacity = 0.5)
+    cam = make_simplified_enzyme_constrained_model(
+        ribomodel;
+        total_gene_product_mass_bound = 0.5,
+    )
 
     @test coupling(cam)[1, 7] == 5.0
 
@@ -71,7 +74,7 @@
 
     # test inplace variant
     add_virtualribosome!(m, "r6", 0.2)
-    cam = m |> with_simplified_enzyme_constraints(total_enzyme_capacity = 0.5)
+    cam = m |> with_simplified_enzyme_constraints(total_gene_product_mass_bound = 0.5)
 
     @test coupling(cam)[1, 7] == 5.0
 

test/reconstruction/enzyme_constrained.jl

@@ -27,7 +27,7 @@
         end
     end
 
-    total_enzyme_capacity = 100.0
+    total_gene_product_mass_bound = 100.0
 
     # set gene product bounds
     for gid in genes(model)
@@ -43,7 +43,7 @@
             lower_bound = [-1000.0, -1.0],
             upper_bound = [nothing, 12.0],
         ) |>
-        with_enzyme_constraints(; total_enzyme_capacity)
+        with_enzyme_constraints(; total_gene_product_mass_bound)
 
     opt_model = flux_balance_analysis(
         gm,
@@ -64,7 +64,7 @@
 
     @test isapprox(
         sum(values(prot_concens)),
-        total_gene_product_mass,
+        total_gene_product_mass_bound,
         atol = TEST_TOLERANCE,
     )
     @test isapprox(

test/reconstruction/simplified_enzyme_constrained.jl

@@ -34,7 +34,7 @@
             lower_bound = [-1000.0, -1.0],
             upper_bound = [nothing, 12.0],
         ) |>
-        with_simplified_enzyme_constraints(total_enzyme_capacity = 100.0)
+        with_simplified_enzyme_constraints(total_gene_product_mass_bound = 100.0)
 
     rxn_fluxes = flux_balance_analysis_dict(
         simplified_enzyme_constrained_model,

test/types/BalancedGrowthCommunityModel.jl

@@ -304,7 +304,7 @@ end
         ecoli |>
         with_added_biomass_metabolite("BIOMASS_Ecoli_core_w_GAM") |>
         with_changed_bounds(["EX_glc__D_e"]; lower_bound = [-1000.0], upper_bound = [0]) |>
-        with_enzyme_constraints(; total_enzyme_capacity = 100.0)
+        with_enzyme_constraints(; total_gene_product_mass_bound = 100.0)
 
     ex_rxns = find_exchange_reaction_ids(ecoli)