fix bugs

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

@@ -133,3 +133,14 @@ ec_solution = enzyme_constrained_flux_balance_analysis(
     0.011875920383431717, #src
     atol = TEST_TOLERANCE, #src
 ) #src
+
+### Running a simplified enzyme constrained model
+
+ec_solution2 = simplified_enzyme_constrained_flux_balance_analysis(
+    model;
+    reaction_isozymes,
+    gene_product_molar_masses,
+    capacity = total_enzyme_capacity,
+    optimizer = Tulip.Optimizer,
+    settings = [set_optimizer_attribute("IPM_IterationsLimit", 10_000)],
+)

src/builders/enzymes.jl

@@ -266,13 +266,13 @@ function add_simplified_enzyme_constraints(
                 sum(
                     stoich * gene_product_molar_masses[gid] for
                     (gid, stoich) in iso.gene_product_stoichiometry
-                ) * iso.kcat_forward for iso in isos
+                ) / iso.kcat_forward for iso in values(isos)
             ),
             reverse = minimum(
                 sum(
                     stoich * gene_product_molar_masses[gid] for
                     (gid, stoich) in iso.gene_product_stoichiometry
-                ) * iso.kcat_reverse for iso in isos
+                ) / iso.kcat_reverse for iso in values(isos)
             ),
         ) for (rid, isos) in reaction_isozymes
     )

src/frontend/enzymes.jl

@@ -29,6 +29,8 @@ the mass of enzymes in the whole model.
 enzymes". Alternatively, `capacity` may be a vector of identifier-genes-limit
 triples that make a constraint (identified by the given identifier) that limits
 the listed genes to the given limit.
+
+Uses [`add_enzyme_constraints`](@ref) internally. 
 """
 function enzyme_constrained_flux_balance_analysis(
     model::A.AbstractFBCModel;
@@ -56,3 +58,50 @@ function enzyme_constrained_flux_balance_analysis(
 end
 
 export enzyme_constrained_flux_balance_analysis
+
+
+
+"""
+$(TYPEDSIGNATURES)
+
+Run a basic simplified enzyme-constrained flux balance analysis on `model`.
+Requires `reaction_isozymes`, which is a mapping of reaction identifiers to
+[`Isozyme`](@ref) descriptions, and `gene_product_molar_masses` which is a
+mapping of gene products to their molar masses. Internally, the cheapest and
+fastest isozyme (minimum of MW/kcat for each isozyme) is used in the capacity
+bound.
+
+`capacity` may be a single number, which sets the limit of protein required for
+all the fluxes in `reaction_isozymes`. Alternatively, `capacity` may be a vector
+of identifier-fluxes-limit triples that make a constraint (identified by the
+given identifier) that limits the enzyme requirements of the listed fluxes to
+the given limit.
+
+Uses [`add_simplified_enzyme_constraints`](@ref) internally. 
+"""
+function simplified_enzyme_constrained_flux_balance_analysis(
+    model::A.AbstractFBCModel;
+    reaction_isozymes::Dict{String,Dict{String,Isozyme}},
+    gene_product_molar_masses::Dict{String,Float64},
+    capacity::Union{Vector{Tuple{String,Vector{String},Float64}},Float64},
+    optimizer,
+    settings = [],
+)
+    constraints = flux_balance_constraints(model)
+
+    constraints = add_simplified_enzyme_constraints(
+        constraints;
+        reaction_isozymes,
+        gene_product_molar_masses,
+        capacity,
+    )
+
+    optimized_constraints(
+        constraints;
+        objective = constraints.objective.value,
+        optimizer,
+        settings,
+    )
+end
+
+export simplified_enzyme_constrained_flux_balance_analysis