Merge pull request #606 from LCSB-BioCore/mo-small-fixes

Small fixes

src/base/types/Gene.jl

@@ -7,7 +7,6 @@ id :: String
 name :: Maybe{String}
 notes :: Dict{String, Vector{String}}
 annotation :: Dict{String, Union{Vector{String}, String}}
-molar_mass :: Maybe{Float64}
 ````
 """
 mutable struct Gene
@@ -15,13 +14,7 @@ mutable struct Gene
     name::Maybe{String}
     notes::Notes
     annotations::Annotations
-    molar_mass::Maybe{Float64}
 
-    Gene(
-        id::String = "";
-        name = nothing,
-        notes = Notes(),
-        annotations = Annotations(),
-        molar_mass = nothing,
-    ) = new(id, name, notes, annotations, molar_mass)
+    Gene(id::String = ""; name = nothing, notes = Notes(), annotations = Annotations()) =
+        new(id, name, notes, annotations)
 end

src/base/types/wrappers/GeckoModel.jl

@@ -55,10 +55,10 @@ The structure contains fields `columns` that describe the contents of the
 coupling columns, `coupling_row_reaction`, `coupling_row_gene_product` and
 `coupling_row_mass_group` that describe correspondence of the coupling rows to
 original model and determine the coupling bounds, and `inner`, which is the
-original wrapped model. Note, `objective` is the objective vector of the model,
-special care needs to be taken to ensure that its length is `n_reactions(model)
-+ n_genes(model)` when the user modifies it, where `model` is the GeckoModel in
-question. 
+original wrapped model. Note, `objective` is the objective vector of the model.
+Special care needs to be taken to ensure that its length is the sum of
+`n_reactions(model)` and `n_genes(model)` when the user modifies it, where
+`model` is the GeckoModel in question.
 
 Implementation exposes the split reactions (available as `reactions(model)`),
 but retains the original "simple" reactions accessible by [`fluxes`](@ref). All

test/analysis/gecko.jl

@@ -46,8 +46,10 @@
     )
 
     prot_mass = sum(ecoli_core_gene_product_masses[gid] * c for (gid, c) in prot_concens)
+    mass_groups = gene_product_mass_group_dict(gm, opt_model)
 
     @test isapprox(prot_mass, total_gene_product_mass, atol = TEST_TOLERANCE)
+    @test isapprox(prot_mass, mass_groups["uncategorized"], atol = TEST_TOLERANCE)
 end
 
 @testset "GECKO small model" begin