cleanup mmdf

Author: exaexa

docs/src/examples/02c-constraint-modifications.jl

@@ -51,7 +51,7 @@ model = load_model("e_coli_core.json")
 
 import ConstraintTrees as C
 
-ctmodel = fbc_model_constraints(model)
+ctmodel = fbc_flux_balance_constraints(model)
 
 fermentation = ctmodel.fluxes.EX_ac_e.value + ctmodel.fluxes.EX_etoh_e.value
 

docs/src/examples/03-parsimonious-flux-balance.jl

@@ -53,7 +53,7 @@ model |> parsimonious_flux_balance_analysis(Clarabel.Optimizer; settings = [sile
 # Alternatively, you can construct your own constraint tree model with
 # the quadratic objective (this approach is much more flexible).
 
-ctmodel = fbc_model_constraints(model)
+ctmodel = fbc_flux_balance_constraints(model)
 ctmodel *= :l2objective^squared_sum_value(ctmodel.fluxes)
 ctmodel.objective.bound = 0.3 # set growth rate # TODO currently breaks
 
@@ -88,7 +88,7 @@ minimize_metabolic_adjustment(ref_sol, Clarabel.Optimizer; settings = [silence])
 # Alternatively, you can construct your own constraint tree model with
 # the quadratic objective (this approach is much more flexible).
 
-ctmodel = fbc_model_constraints(model)
+ctmodel = fbc_flux_balance_constraints(model)
 ctmodel *=
     :minoxphospho^squared_sum_error_value(
         ctmodel.fluxes,

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

@@ -140,7 +140,7 @@ ec_solution = enzyme_constrained_flux_balance_analysis(
 import ConstraintTrees as C
 
 # create basic flux model
-m = fbc_model_constraints(model)
+m = fbc_flux_balance_constraints(model)
 
 # create enzyme variables
 m += :enzymes^gene_product_variables(model)

docs/src/examples/07-loopless-models.jl

@@ -61,7 +61,7 @@ sol = loopless_flux_balance_analysis(model; optimizer = GLPK.Optimizer)
 # not use the convenience function), let's build a loopless model from scratch.
 
 # First, build a normal flux balance model
-m = fbc_model_constraints(model)
+m = fbc_flux_balance_constraints(model)
 
 # Next, find all internal reactions, and their associated indices for use later
 internal_reactions = [

docs/src/examples/08-community-models.jl

@@ -51,8 +51,8 @@ model = load_model("e_coli_core.json")
 # because it is easier to build the model explicitly than rely on an opaque
 # one-shot function.
 
-ecoli1 = fbc_model_constraints(model)
-ecoli2 = fbc_model_constraints(model)
+ecoli1 = fbc_flux_balance_constraints(model)
+ecoli2 = fbc_flux_balance_constraints(model)
 
 # Since the models are joined through their individual exchange reactions to an
 # environmental exchange reactionq, we need to identify all possible exchange

src/builders/fbc.jl

@@ -25,7 +25,7 @@ The constructed tree contains subtrees `fluxes` (with the reaction-defining
 constraints), and a single constraint `objective` thad describes the objective
 function of the model.
 """
-function fbc_model_constraints(model::A.AbstractFBCModel)
+function fbc_flux_balance_constraints(model::A.AbstractFBCModel)
     rxns = Symbol.(A.reactions(model))
     mets = Symbol.(A.metabolites(model))
     lbs, ubs = A.bounds(model)
@@ -34,7 +34,7 @@ function fbc_model_constraints(model::A.AbstractFBCModel)
     obj = A.objective(model)
 
     return C.ConstraintTree(
-        :fluxes^C.variables(keys = rxns, bounds = zip(lbs, ubs)) *
+        :fluxes^C.variables(keys = reactions, bounds = zip(lbs, ubs)) *
         :flux_stoichiometry^C.ConstraintTree(
             met => C.Constraint(
                 value = C.LinearValue(SparseArrays.sparse(row)),
@@ -45,4 +45,38 @@ function fbc_model_constraints(model::A.AbstractFBCModel)
     )
 end
 
-export fbc_model_constraints
+export fbc_flux_balance_constraints
+
+"""
+$(TYPEDSIGNATURES)
+
+TODO
+"""
+function fbc_log_concentration_constraints(
+    model::A.AbstractFBCModel;
+    concentration_bound = _ -> nothing,
+)
+    rxns = Symbol.(A.reations(model))
+    mets = Symbol.(A.metabolites(model))
+    stoi = A.stoichiometry(model)
+
+    constraints =
+        :log_concentrations^C.variables(keys = mets, bounds = concentration_bound.(mets)) +
+        :reactant_log_concentrations^C.variables(keys = rxns)
+
+    cs = C.ConstraintTree()
+
+    for (midx, ridx, coeff) in zip(findnz(stoi)...)
+        rid = rxns[ridx]
+        value = constraints.log_concentrations[mets[midx]] * coeff
+        if haskey(cs, rid)
+            cs[rid].value += value
+        else
+            cs[rid] = C.Constraint(; value)
+        end
+    end
+
+    return constraints * :concentration_stoichiometry^cs
+end
+
+export fbc_log_concentration_constraints

src/builders/mmdf.jl

@@ -22,10 +22,10 @@ Compute an optimal objective-optimizing solution of the given `model`.
 Most arguments are forwarded to [`optimized_constraints`](@ref).
 
 Returns a tree with the optimization solution of the same shape as
-given by [`fbc_model_constraints`](@ref).
+given by [`fbc_flux_balance_constraints`](@ref).
 """
 function flux_balance_analysis(model::A.AbstractFBCModel, optimizer; kwargs...)
-    constraints = fbc_model_constraints(model)
+    constraints = fbc_flux_balance_constraints(model)
     optimized_constraints(
         constraints;
         objective = constraints.objective.value,

src/frontend/balance.jl

@@ -55,7 +55,7 @@ function enzyme_constrained_flux_balance_analysis(
     optimizer,
     settings = [],
 )
-    constraints = fbc_model_constraints(model)
+    constraints = fbc_flux_balance_constraints(model)
 
     # might be nice to omit some conditionally (e.g. slash the direction if one
     # kcat is nothing)

src/frontend/enzyme_constrained.jl

@@ -45,7 +45,7 @@ function loopless_flux_balance_analysis(
     optimizer,
 )
 
-    m = fbc_model_constraints(model)
+    m = fbc_flux_balance_constraints(model)
 
     # find all internal reactions
     internal_reactions = [