delete MMDF analysis and move to wrapper

src/analysis/max_min_driving_force.jl → src/types/wrappers/ThermodynamicModel.jl

@@ -1,3 +1,69 @@
+"""
+$(TYPEDEF)
+
+# Fields
+$(TYPEDFIELDS)
+"""
+Base.@kwdef mutable struct ThermodynamicModel <: AbstractModelWrapper
+    "A dictionary mapping ΔrG⁰ to reactions."
+    reaction_standard_gibbs_free_energies::Dict{String,Float64} = Dict{String,Float64}()
+
+    "A reference flux solution that is used to set the directions of the reactions."
+    flux_solution::Dict{String,Float64} = Dict{String,Float64}()
+
+    "Metabolite ids of protons."
+    proton_ids::Vector{String} = ["h_c", "h_e"]
+
+    "Metabolite ids of water."
+    water_ids::Vector{String} = ["h2o_c", "h2o_e"]
+
+    "A dictionationay mapping metabolite ids to concentrations."
+    constant_concentrations::Dict{String,Float64} = Dict{String,Float64}()
+
+    "A dictionary mapping metabolite ids to concentration ratios in the form `(m1, m2) = r === m1/m2 = r`."
+    concentration_ratios::Dict{Tuple{String,String},Float64} = Dict{
+        Tuple{String,String},
+        Float64,
+    }()
+
+    "Global metabolite concentration lower bound."
+    concentration_lb = 1e-9
+
+    "Global metabolite concentration upper bound."
+    concentration_ub = 100e-3
+
+    "Thermodynamic temperature."
+    T::Float64 = constants.T
+
+    "Real gas constant."
+    R::Float64 = constants.R
+
+    "Tolerance use to distinguish flux carrying reactions from zero flux reactions."
+    small_flux_tol::Float64 = 1e-6
+
+    "Reaction ids that are ignored internally during thermodynamic calculations."
+    ignore_reaction_ids::Vector{String} = String[]
+
+    "Inner metabolic model calculations are based on."
+    inner::AbstractMetabolicModel
+end
+
+Accessors.unwrap_model(model::ThermodynamicModel) = model.inner
+
+
+Accessors.n_reactions(tm::ThermodynamicModel) 
+
+Accessors.reactions(tm::ThermodynamicModel) 
+
+Accessors.n_metabolites(tm::ThermodynamicModel) 
+
+Accessors.metabolites(tm::ThermodynamicModel) 
+
+Accessors.bounds(tm::ThermodynamicModel) 
+
+Accessors.stoichiometry(tm::ThermodynamicModel) 
+
+
 """
 $(TYPEDSIGNATURES)