move log concentration to mmdf builder

src/COBREXA.jl

@@ -71,6 +71,7 @@ include("builders/loopless.jl")
 include("builders/objectives.jl")
 include("builders/scale.jl")
 include("builders/unsigned.jl")
+include("builders/mmdf.jl")
 
 # simplified front-ends for the above
 include("frontend/balance.jl")

src/builders/fbc.jl

@@ -109,46 +109,3 @@ function flux_balance_constraints(
 end
 
 export flux_balance_constraints
-
-"""
-$(TYPEDSIGNATURES)
-
-Build log-concentration-stoichiometry constraints for the `model`, as used e.g.
-by [`max_min_driving_force_analysis`](@ref).
-
-The output constraint tree contains a log-concentration variable for each
-metabolite in subtree `log_concentrations`. Individual reactions' total
-reactant log concentrations (i.e., all log concentrations of actual reactants
-minus all log concentrations of products) have their own variables in
-`reactant_log_concentrations`.
-
-Function `concentration_bound` may return a bound for the log-concentration of
-a given metabolite (compatible with `ConstraintTrees.Bound`), or `nothing`.
-"""
-function log_concentration_constraints(
-    model::A.AbstractFBCModel;
-    concentration_bound = _ -> nothing,
-)
-    rxns = Symbol.(A.reactions(model))
-    mets = Symbol.(A.metabolites(model))
-    stoi = A.stoichiometry(model)
-
-    constraints =
-        :log_concentrations^C.variables(keys = mets, bounds = concentration_bound.(mets))
-
-    cs = C.ConstraintTree()
-
-    for (midx, ridx, coeff) in zip(SparseArrays.findnz(stoi)...)
-        rid = rxns[ridx]
-        value = constraints.log_concentrations[mets[midx]].value * coeff
-        if haskey(cs, rid)
-            cs[rid].value += value
-        else
-            cs[rid] = C.Constraint(; value)
-        end
-    end
-
-    return constraints * :reactant_log_concentrations^cs
-end
-
-export log_concentration_constraints

src/builders/mmdf.jl

@@ -0,0 +1,58 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+$(TYPEDSIGNATURES)
+
+Build log-concentration-stoichiometry constraints for the `model`, as used e.g.
+by [`max_min_driving_force_analysis`](@ref).
+
+The output constraint tree contains a log-concentration variable for each
+metabolite in subtree `log_concentrations`. Individual reactions' total
+reactant log concentrations (i.e., all log concentrations of actual reactants
+minus all log concentrations of products) have their own variables in
+`reactant_log_concentrations`.
+
+Function `concentration_bound` may return a bound for the log-concentration of
+a given metabolite (compatible with `ConstraintTrees.Bound`), or `nothing`.
+"""
+function log_concentration_constraints(
+    model::A.AbstractFBCModel;
+    concentration_bound = _ -> nothing,
+)
+    rxns = Symbol.(A.reactions(model))
+    mets = Symbol.(A.metabolites(model))
+    stoi = A.stoichiometry(model)
+
+    constraints =
+        :log_concentrations^C.variables(keys = mets, bounds = concentration_bound.(mets))
+
+    cs = C.ConstraintTree()
+
+    for (midx, ridx, coeff) in zip(SparseArrays.findnz(stoi)...)
+        rid = rxns[ridx]
+        value = constraints.log_concentrations[mets[midx]].value * coeff
+        if haskey(cs, rid)
+            cs[rid].value += value
+        else
+            cs[rid] = C.Constraint(; value)
+        end
+    end
+
+    return constraints * :reactant_log_concentrations^cs
+end
+
+export log_concentration_constraints