From 7f0fc9d252d9883e7e30ceebcaffbc46aae2ecb6 Mon Sep 17 00:00:00 2001
From: stelmo <stelmozors@gmail.com>
Date: Thu, 1 Apr 2021 14:47:49 +0200
Subject: [PATCH] added constraint modification callback
---
src/analysis/fba.jl | 23 ++++++++++++-----------
src/base/utilities.jl | 12 ++++++++++++
2 files changed, 24 insertions(+), 11 deletions(-)
diff --git a/src/analysis/fba.jl b/src/analysis/fba.jl
index f5adcfdd3..7b9beed1e 100644
--- a/src/analysis/fba.jl
+++ b/src/analysis/fba.jl
@@ -65,16 +65,23 @@ sol = fba(model, biomass, optimizer; solver_attributes=atts)
function fba(
model::CobraModel,
optimizer;
- objective_func::Union{Reaction,Array{Reaction,1}} = Reaction[],
- weights = Float64[],
- solver_attributes = Dict{Any,Any}(),
- constraints = Dict{String,Tuple{Float64,Float64}}(),
- sense = MOI.MAX_SENSE,
+ modifications = [(model, opt_model)->nothing]
)
+
+objective_func::Union{Reaction,Array{Reaction,1}} = Reaction[]
+weights = Float64[]
+solver_attributes = Dict{Any,Any}()
+sense = MOI.MAX_SENSE
+
# get core optimization problem
cbm = make_optimization_model(model, optimizer, sense = sense)
v = cbm[:x] # fluxes
+ # apply callbacks
+ for mod in modifications
+ mod(model, cbm)
+ end
+
# modify core optimization problem according to user specifications
if !isempty(solver_attributes) # set other attributes
for (k, val) in solver_attributes
@@ -82,12 +89,6 @@ function fba(
end
end
- # set additional constraints
- for (rxnid, con) in constraints
- ind = model.reactions[findfirst(model.reactions, rxnid)]
- set_bound(ind, cbm; lb = con[1], ub = con[2])
- end
-
# if an objective function is supplied, modify the default objective
if typeof(objective_func) == Reaction || !isempty(objective_func)
# ensure that an array of objective indices are fed in
diff --git a/src/base/utilities.jl b/src/base/utilities.jl
index ac473dd56..e2d6d7233 100644
--- a/src/base/utilities.jl
+++ b/src/base/utilities.jl
@@ -34,3 +34,15 @@ function set_bound(vind, opt_model; ub = 1000, lb = -1000)
end
set_normalized_rhs(opt_model[:ubs][vind], ub)
end
+
+"""
+ modify_constraint(reaction::Reaction, lb, ub)
+
+Modify constraints of model reaction.
+"""
+function modify_constraint(reaction::Reaction, lb, ub)
+ (model, opt_model) -> begin
+ ind = model.reactions[reaction]
+ set_bound(ind, opt_model, lb=lb, ub=ub)
+ end
+end
--
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