From b90df728e88ee028c66167e7ee82c3770746d766 Mon Sep 17 00:00:00 2001
From: Mirek Kratochvil <exa.exa@gmail.com>
Date: Mon, 30 Aug 2021 16:14:22 +0200
Subject: [PATCH] improve parametrization of objective_envelope
---
src/analysis/envelopes.jl | 36 ++++++++++++++++++++++++------------
1 file changed, 24 insertions(+), 12 deletions(-)
diff --git a/src/analysis/envelopes.jl b/src/analysis/envelopes.jl
index 7c699d2ea..ce628a83b 100644
--- a/src/analysis/envelopes.jl
+++ b/src/analysis/envelopes.jl
@@ -51,8 +51,10 @@ objective_envelope(model::MetabolicModel, rids::Vector{String}, args...; kwargs.
model::MetabolicModel,
ridxs::Vector{Int},
optimizer;
+ modifications = [],
lattice_args = (),
lattice = envelope_lattice(model, ridxs; lattice_args...),
+ analysis = screen_optimize_objective,
kwargs...,
)
@@ -62,11 +64,11 @@ lower and upper bounds.
This can be used to compute a "production envelope" of a metabolite; but
generalizes to any specifiable objective and to multiple dimensions of the
-examined space. To retrieve a production envelope of any metabolite, set the
-objective coefficient vector of the `model` to a vector that contains a single
-`1` for the exchange reaction that "outputs" this metabolite, and run
-[`objective_envelope`](@ref) with the exchange reaction of the "parameter"
-metabolite specified in `ridxs`.
+examined space. For example, to retrieve a production envelope of any
+metabolite, set the objective coefficient vector of the `model` to a vector
+that contains a single `1` for the exchange reaction that "outputs" this
+metabolite, and run [`objective_envelope`](@ref) with the exchange reaction of
+the "parameter" metabolite specified in `ridxs`.
Returns a named tuple that contains `lattice` with reference values of the
metabolites, and an N-dimensional array `values` with the computed objective
@@ -78,6 +80,9 @@ the model and reaction indexes. Additional arguments for the call to
[`envelope_lattice`](@ref) can be optionally specified in `lattice_args`.
`kwargs` are internally forwarded to [`screen_optmodel_modifications`](@ref).
+`modifications` are appended to the list of modifications after the lattice
+bounds are set. By default, this returns the objective values for all points in
+the lattice; alternate outputs can be implemented via the `analysis` argument.
# Example
```
@@ -106,8 +111,10 @@ objective_envelope(
model::MetabolicModel,
ridxs::Vector{Int},
optimizer;
+ modifications = [],
lattice_args = (),
lattice = envelope_lattice(model, ridxs; lattice_args...),
+ analysis = screen_optimize_objective,
kwargs...,
) = (
lattice = collect.(lattice),
@@ -115,14 +122,19 @@ objective_envelope(
model,
optimizer;
modifications = collect(
- [(_, optmodel) -> begin
- for (i, ridx) in enumerate(ridxs)
- set_normalized_rhs(optmodel[:lbs][ridx], fluxes[i])
- set_normalized_rhs(optmodel[:ubs][ridx], fluxes[i])
- end
- end] for fluxes in Iterators.product(lattice...)
+ vcat(
+ [
+ (_, optmodel) -> begin
+ for (i, ridx) in enumerate(ridxs)
+ set_normalized_rhs(optmodel[:lbs][ridx], fluxes[i])
+ set_normalized_rhs(optmodel[:ubs][ridx], fluxes[i])
+ end
+ end,
+ ],
+ modifications,
+ ) for fluxes in Iterators.product(lattice...)
),
- analysis = screen_optimize_objective,
+ analysis = analysis,
kwargs...,
),
)
--
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