WIP

src/frontend/mmdf.jl

@@ -49,7 +49,7 @@ Reactions specified in `ignore_reaction_ids` are internally ignored when
 calculating the max-min driving force. Importantly, this should include water
 and proton importers.
 
-Since biochemical thermodynamics are assumed, the `proton_ids` and `water_ids`
+Since biochemical thermodynamics are assumed, the `proton_metabolites` and `water_metabolites`
 need to be specified so that they can be ignored in the calculations.
 Effectively this assumes an aqueous environment at constant pH is used.
 
@@ -75,16 +75,83 @@ function max_min_driving_force_analysis(
     reference_flux = Dict{String,Float64}(),
     concentration_ratios = Dict{String,Tuple{String,String,Float64}}(),
     constant_concentrations = Dict{String,Float64}(),
-    proton_ids,
-    water_ids,
+    ignored_metabolites = Set{String}()proton_metabolites = Set{String}(),
+    water_metabolites = Set{String}(),
     concentration_lb = 1e-9, # M
     concentration_ub = 1e-1, # M
     T = 298.15, # Kelvin
     R = 8.31446261815324e-3, # kJ/K/mol
-    ignore_reaction_ids = String[],
+    check_ignored_reactions = missing,
     settings = [],
     optimizer,
 )
+
+    # First let's check if all the identifiers are okay because we use quite a
+    # lot of these.
+
+    model_reactions = Set(A.reactions(model))
+    model_metabolites = Set(A.metabolites(model))
+
+    all(in(model_reactions), keys(reaction_standard_gibbs_free_energies)) || throw(
+        DomainError(
+            reaction_standard_gibbs_free_energies,
+            "unknown reactions referenced by reaction_standard_gibbs_free_energies",
+        ),
+    )
+    all(in(model_reactions), keys(reference_flux)) || throw(
+        DomainError(
+            reaction_standard_gibbs_free_energies,
+            "unknown reactions referenced by reference_flux",
+        ),
+    )
+    all(in(model_metabolites), keys(constant_concentrations)) || throw(
+        DomainError(
+            constant_concentrations,
+            "unknown metabolites referenced by constant_concentrations",
+        ),
+    )
+    all(
+        in(model_metabolites),
+        (m for (_, (x, y, _)) in concentration_ratios for m in (x, y)),
+    ) || throw(
+        DomainError(
+            concentration_ratios,
+            "unknown metabolites referenced by concentration_ratios",
+        ),
+    )
+    all(in(model_metabolites), proton_metabolites) || throw(
+        DomainError(
+            concentration_ratios,
+            "unknown metabolites referenced by proton_metabolites",
+        ),
+    )
+    all(in(model_metabolites), water_metabolites) || throw(
+        DomainError(
+            concentration_ratios,
+            "unknown metabolites referenced by water_metabolites",
+        ),
+    )
+    all(in(model_metabolites), ignored_metabolites) || throw(
+        DomainError(
+            concentration_ratios,
+            "unknown metabolites referenced by ignored_metabolites",
+        ),
+    )
+
+    if !ismissing(check_ignored_reactions) && (
+        all(
+            x -> !haskey(reaction_standard_gibbs_free_energies, x),
+            check_ignored_reactions,
+        ) || (
+            union(
+                Set(check_ignored_reactions),
+                Set(keys(reaction_standard_gibbs_free_energies)),
+            ) != model_reactions
+        )
+    )
+        throw(AssertionError("check_ignored_reactions validation failed"))
+    end
+
     m = max_min_driving_force_constraints(
         model,
         reaction_standard_gibbs_free_energies;
@@ -94,8 +161,8 @@ function max_min_driving_force_analysis(
         R,
         T,
         ignore_reaction_ids,
-        water_ids,
-        proton_ids,
+        water_metabolites,
+        proton_metabolites,
     )
 
     for (mid, val) in constant_concentrations