From 3b1b805de5db816c1d6bea096a9b34ceb7686335 Mon Sep 17 00:00:00 2001
From: "St. Elmo" <stelmozors@gmail.com>
Date: Fri, 18 Jun 2021 20:22:57 +0200
Subject: [PATCH] update reaction
---
src/base/types/Reaction.jl | 132 ++++++++++++++++++-------------------
1 file changed, 65 insertions(+), 67 deletions(-)
diff --git a/src/base/types/Reaction.jl b/src/base/types/Reaction.jl
index a27039d47..3f07664c5 100644
--- a/src/base/types/Reaction.jl
+++ b/src/base/types/Reaction.jl
@@ -1,4 +1,4 @@
-using Base: Float64
+using Base: kwarg_decl
"""
Reaction struct.
@@ -27,32 +27,60 @@ mutable struct Reaction
notes::Notes
annotations::Annotations
objective_coefficient::Float64
-
- Reaction(
- id = "";
- name = nothing,
- metabolites = Dict{String,Float64}(),
- lb = -_constants.default_reaction_bound,
- ub = _constants.default_reaction_bound,
- grr = nothing,
- subsystem = nothing,
- notes = Notes(),
- annotations = Annotations(),
- objective_coefficient = 0.0,
- ) = new(
- id,
- name,
- metabolites,
- lb,
- ub,
- grr,
- subsystem,
- notes,
- annotations,
- objective_coefficient,
- )
end
+"""
+Reaction(
+ id = "";
+ name = nothing,
+ metabolites = Dict{String,Float64}(),
+ lb = -_constants.default_reaction_bound,
+ ub = _constants.default_reaction_bound,
+ grr = nothing,
+ subsystem = nothing,
+ notes = Notes(),
+ annotations = Annotations(),
+ objective_coefficient = 0.0,
+)
+
+A constructor for Reaction that only takes a reaction `id` and
+assigns default/uninformative values to all the fields that are not
+explicitely assigned.
+"""
+Reaction(
+ id = "";
+ name = nothing,
+ metabolites = Dict{String,Float64}(),
+ lb = -_constants.default_reaction_bound,
+ ub = _constants.default_reaction_bound,
+ grr = nothing,
+ subsystem = nothing,
+ notes = Notes(),
+ annotations = Annotations(),
+ objective_coefficient = 0.0,
+) = Reaction(
+ id,
+ name,
+ metabolites,
+ lb,
+ ub,
+ grr,
+ subsystem,
+ notes,
+ annotations,
+ objective_coefficient,
+)
+
+Reaction(
+ id::String;
+ metabolites = Dict{String,Real}(),
+ kwargs...
+) = Reaction(
+ id;
+ Dict(k => float(v) for (k, v) in metabolites),
+ kwargs...
+)
+
"""
Reaction(
id::String,
@@ -61,7 +89,12 @@ Reaction(
default_bound = _constants.default_reaction_bound,
)
-Convenience constructor for `Reaction`.
+Convenience constructor for `Reaction`. The reaction equation is specified using
+`metabolites`, which is a dictionary mapping metabolite ids to stoichiometric
+coefficients. The direcion of the reaction is set through `dir` which can take
+`:bidirectional`, `:forward`, and `:reverse` as values. Finally, the
+`default_bound` is the value taken to mean infinity in the context of constraint
+based models, often this is set to a very high flux value like 1000.
"""
function Reaction(
id::String,
@@ -90,7 +123,12 @@ Reaction(
default_bound = _constants.default_reaction_bound,
)
-Convenience constructor for `Reaction`.
+Convenience constructor for `Reaction`. The reaction equation is specified using
+`metabolites`, which is a dictionary mapping metabolite ids to stoichiometric
+coefficients. The direcion of the reaction is set through `dir` which can take
+`:bidirectional`, `:forward`, and `:reverse` as values. Finally, the
+`default_bound` is the value taken to mean infinity in the context of constraint
+based models, often this is set to a very high flux value like 1000.
"""
Reaction(
id::String,
@@ -103,43 +141,3 @@ Reaction(
dir;
default_bound = default_bound,
)
-
-"""
-Reaction(
- id::String;
- name = nothing,
- metabolites = Dict{String,Real}(),
- lb = -_constants.default_reaction_bound,
- ub = _constants.default_reaction_bound,
- grr = nothing,
- subsystem = nothing,
- notes = Notes(),
- annotations = Annotations(),
- objective_coefficient = 0.0,
-)
-
-Convenience constructor for `Reaction`.
-"""
-Reaction(
- id::String;
- name = nothing,
- metabolites = Dict{String,Real}(),
- lb = -_constants.default_reaction_bound,
- ub = _constants.default_reaction_bound,
- grr = nothing,
- subsystem = nothing,
- notes = Notes(),
- annotations = Annotations(),
- objective_coefficient = 0.0,
-) = Reaction(
- id,
- name,
- Dict(k => float(v) for (k, v) in metabolites),
- lb,
- ub,
- grr,
- subsystem,
- notes,
- annotations,
- objective_coefficient,
-)
--
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