diff --git a/docs/src/notebooks/5_basic_stdmodel_construction.jl b/docs/src/notebooks/5_basic_stdmodel_construction.jl
index 0df1ab33fc387817b3629ebeedd1f337eb957d27..3473b957c3f19f8e0c2e8a7e00610afffe0af0fd 100644
--- a/docs/src/notebooks/5_basic_stdmodel_construction.jl
+++ b/docs/src/notebooks/5_basic_stdmodel_construction.jl
@@ -41,7 +41,7 @@ add_metabolites!(model, metabolite_list)
# There are two ways to create and add reactions to a model.
# These are using functions, or macros.
-r_m1 = Reaction("EX_m1", Dict("m1" => -1.0), :bidirectional) # exchange reaction: m1 <-> (is the same as m1 ⟷ nothing)
+r_m1 = Reaction("EX_m1", Dict("m1" => -1.0), :bidirectional) # exchange reaction: m1 <-> (is the same as m1 ↔ nothing)
r1 = Reaction("r1", Dict("m1" => -1.0, "m2" => 1.0), :forward)
r1.grr = [["g1", "g2"], ["g3"]] # add some gene reaction rules
r2 = Reaction("r2", Dict("m2" => -1.0, "m1" => 1.0), :backward)
@@ -55,28 +55,14 @@ m3 = metabolite_list[3]
m4 = metabolite_list[4]
@add_reactions! model begin # macro approach
- "r4", m2 ⟶ m4, 0, 1000
- "r_m3", m3 ⟷ nothing, -1000, 1000
- "r_m4", m4 ⟶ nothing
- "r5", m4 ⟶ m2
+ "r4", m2 → m4, 0, 1000
+ "r_m3", m3 ↔ nothing, -1000, 1000
+ "r_m4", m4 → nothing
+ "r5", m4 → m2
end
model.reactions["r4"].grr = [["g5"], ["g6", "g7"], ["g8"]]
-#md # !!! note "Note: Using reaction arrows"
-#md # `COBREXA` exports arrows that can be used to construct reactions.
-#md # Both the long and short arrows (`⟶ == →`) mean the same thing if they
-#md # point in the same direction.
-#md #
-#md # These arrows are accessible by using the `LaTeX` completions built into
-#md # Julia. For example:
-#md # 1. → is \rightarrow<tab>
-#md # 2. ⟶ is \longrightarrow<tab>
-#md # 3. ↠is \leftarrow<tab>
-#md # 4. ⟵ is \longleftarrow<tab>
-#md # 5. ↔ is \leftrightarrow<tab>
-#md # 6. ⟷ is \longleftrightarrow<tab>
-
# The constructed model can now be inspected.
model
diff --git a/src/analysis/flux_balance_analysis.jl b/src/analysis/flux_balance_analysis.jl
index a677d3f7ad8cfecc4006531b6ed901f28f07b3cb..0afd5b56cd9308ed9a35dfbd3b0578097090385d 100644
--- a/src/analysis/flux_balance_analysis.jl
+++ b/src/analysis/flux_balance_analysis.jl
@@ -43,7 +43,7 @@ s.t. S x = b
xₗ ≤ x ≤ xᵤ
```
See "Orth, J., Thiele, I. & Palsson, B. What is flux balance analysis?. Nat
-Biotechnol 28, 245–248 (2010). https://doi.org/10.1038/nbt.1614" for more
+Biotechnol 28, 245-248 (2010). https://doi.org/10.1038/nbt.1614" for more
information.
The `optimizer` must be set to a `JuMP`-compatible optimizer, such as
diff --git a/src/analysis/modifications/optimizer.jl b/src/analysis/modifications/optimizer.jl
index 7c27b4aa0fc54a03926790254275ab92374a0f99..556d5d5fda8dddc5e6d530a5617317a97ae289ff 100644
--- a/src/analysis/modifications/optimizer.jl
+++ b/src/analysis/modifications/optimizer.jl
@@ -45,9 +45,9 @@ with [`objective_bounds`](@ref).
"""
function constrain_objective_value(tolerance)
return (model, opt_model) -> begin
- λmin, λmax = objective_bounds(tolerance)(objective_value(opt_model))
+ lambda_min, lambda_max = objective_bounds(tolerance)(objective_value(opt_model))
old_objective = objective_function(opt_model)
- @constraint(opt_model, λmin <= sum(old_objective) <= λmax)
+ @constraint(opt_model, lambda_min <= sum(old_objective) <= lambda_max)
end
end
diff --git a/src/analysis/parsimonious_flux_balance_analysis.jl b/src/analysis/parsimonious_flux_balance_analysis.jl
index 1ca7eea01fa2cdb73e10a3e686621262a0eea0b1..24752459a1251b4ca84bde25889f6dd34e25169a 100644
--- a/src/analysis/parsimonious_flux_balance_analysis.jl
+++ b/src/analysis/parsimonious_flux_balance_analysis.jl
@@ -24,10 +24,10 @@ s.t. S x = b
Where the optimal solution of the FBA problem, μâ°, has been added as an
additional constraint. See "Lewis, Nathan E, Hixson, Kim K, Conrad, Tom M,
Lerman, Joshua A, Charusanti, Pep, Polpitiya, Ashoka D, Adkins, Joshua N,
-Schramm, Gunnar, Purvine, Samuel O, Lopezâ€Ferrer, Daniel, Weitz, Karl K, Eils,
+Schramm, Gunnar, Purvine, Samuel O, Lopez-Ferrer, Daniel, Weitz, Karl K, Eils,
Roland, König, Rainer, Smith, Richard D, Palsson, Bernhard Ø, (2010) Omic data
from evolved E. coli are consistent with computed optimal growth from
-genomeâ€scale models. Molecular Systems Biology, 6. 390. doi:
+genome-scale models. Molecular Systems Biology, 6. 390. doi:
accession:10.1038/msb.2010.47" for more details.
pFBA gets the model optimum by standard FBA (using
diff --git a/src/analysis/sampling/affine_hit_and_run.jl b/src/analysis/sampling/affine_hit_and_run.jl
index 899364eabbf2f4b2a5e4acfc884348fa582870e5..4c7992d0f57c0f03974a05b0e73fdec8a3bb8aa0 100644
--- a/src/analysis/sampling/affine_hit_and_run.jl
+++ b/src/analysis/sampling/affine_hit_and_run.jl
@@ -99,8 +99,8 @@ function _affine_hit_and_run_chain(warmup, lbs, ubs, iters, chain)
# iteratively collect the maximum and minimum possible multiple
# of `dir` added to the current point
- λmax = Inf
- λmin = -Inf
+ lambda_max = Inf
+ lambda_min = -Inf
for j = 1:d
dl = lbs[j] - points[j, i]
du = ubs[j] - points[j, i]
@@ -115,13 +115,13 @@ function _affine_hit_and_run_chain(warmup, lbs, ubs, iters, chain)
lower = -Inf
upper = Inf
end
- λmin = max(λmin, lower)
- λmax = min(λmax, upper)
+ lambda_min = max(lambda_min, lower)
+ lambda_max = min(lambda_max, upper)
end
- λ = λmin + rand() * (λmax - λmin)
- !isfinite(λ) && continue # avoid divergence
- new_points[:, i] = points[:, i] .+ λ .* dir
+ lambda = lambda_min + rand() * (lambda_max - lambda_min)
+ !isfinite(lambda) && continue # avoid divergence
+ new_points[:, i] = points[:, i] .+ lambda .* dir
# TODO normally, here we would check if sum(S*new_point) is still
# lower than the tolerance, but we shall trust the computer
diff --git a/src/io/show/Reaction.jl b/src/io/show/Reaction.jl
index 4513438740378691c4f378e4cdd54bf6ba387968..b82c08329b00e697e270709a2084ddb7cd5d9704 100644
--- a/src/io/show/Reaction.jl
+++ b/src/io/show/Reaction.jl
@@ -16,13 +16,13 @@ end
function Base.show(io::IO, ::MIME"text/plain", r::Reaction)
if r.ub > 0.0 && r.lb < 0.0
- arrow = " ⟷ "
+ arrow = " ↔ "
elseif r.ub <= 0.0 && r.lb < 0.0
- arrow = " ⟵ "
+ arrow = " ↠"
elseif r.ub > 0.0 && r.lb >= 0.0
- arrow = " ⟶ "
+ arrow = " → "
else
- arrow = " →∣↠" # blocked reaction
+ arrow = " →|↠" # blocked reaction
end
substrates =
["$(-v) $k" for (k, v) in Iterators.filter(((_, v)::Pair -> v < 0), r.metabolites)]
diff --git a/src/reconstruction/CoreModel.jl b/src/reconstruction/CoreModel.jl
index eacc8296b50dc076d89003729d7ba5eea4203eb6..4ecea9508f2ee6ddc0c166797294a7f3f8144876 100644
--- a/src/reconstruction/CoreModel.jl
+++ b/src/reconstruction/CoreModel.jl
@@ -290,7 +290,7 @@ m4 = remove_metabolites(model, first(indexin(["glc__D_e"], metabolites(model))))
```
"""
function remove_metabolites(model::CoreModel, mets)
- mets_to_keep = filter(x -> x ∉ mets, 1:n_metabolites(model))
+ mets_to_keep = filter(!in(mets), 1:n_metabolites(model))
temp_S = model.S[mets_to_keep, :]
(I, rxns_to_keep, val) = findnz(temp_S)
@@ -331,7 +331,7 @@ Removes a set of reactions from a CoreModel.
Also removes the metabolites not involved in any reaction.
"""
function remove_reactions(m::CoreModel, rxns::Vector{Int})
- rxns_to_keep = filter(e -> e ∉ rxns, 1:n_reactions(m))
+ rxns_to_keep = filter(!in(rxns), 1:n_reactions(m))
temp_s = m.S[:, rxns_to_keep]
(mets_to_keep, J, val) = findnz(temp_s)
diff --git a/src/reconstruction/CoreModelCoupled.jl b/src/reconstruction/CoreModelCoupled.jl
index 1cfb13fecb951f4ce1acd7894af88fb9f6aca121..02f7f460cd783e1a8392bbef9fc81f4f032bbdab 100644
--- a/src/reconstruction/CoreModelCoupled.jl
+++ b/src/reconstruction/CoreModelCoupled.jl
@@ -175,7 +175,7 @@ Also removes any metabolites not involved in any reaction after the deletion.
function remove_reactions(m::CoreModelCoupled, rxns::Vector{Int})
return CoreModelCoupled(
remove_reactions(m.lm, rxns),
- m.C[:, filter(e -> e ∉ rxns, 1:n_reactions(m))],
+ m.C[:, filter(!in(rxns), 1:n_reactions(m))],
m.cl,
m.cu,
)
@@ -319,7 +319,7 @@ Removes a set of coupling constraints from a [`CoreModelCoupled`](@ref)
in-place.
"""
function remove_coupling_constraints!(m::CoreModelCoupled, constraints::Vector{Int})
- to_be_kept = filter(e -> e ∉ constraints, 1:n_coupling_constraints(m))
+ to_be_kept = filter(!in(constraints), 1:n_coupling_constraints(m))
m.C = m.C[to_be_kept, :]
m.cl = m.cl[to_be_kept]
m.cu = m.cu[to_be_kept]
@@ -343,7 +343,7 @@ function change_coupling_bounds!(
cl::V = Float64[],
cu::V = Float64[],
) where {V<:VecType}
- found = [index ∈ 1:n_coupling_constraints(model) for index in constraints]
+ found = (constraints .>= 1) .& (constraints .<= n_coupling_constraints(model))
red_constraints = constraints[found]
length(red_constraints) == length(unique(red_constraints)) ||
diff --git a/src/reconstruction/Reaction.jl b/src/reconstruction/Reaction.jl
index d26ed6ff814f2e708aa3d8e84001d006f3fd16a8..834651c574a796158635d2777f71983c6ee2e221 100644
--- a/src/reconstruction/Reaction.jl
+++ b/src/reconstruction/Reaction.jl
@@ -62,7 +62,7 @@ function _mkrxn(substrates, products)
end
"""
- ⟶(
+ →(
substrates::Union{
Nothing,
Metabolite,
@@ -78,9 +78,8 @@ end
)
Make a forward-only [`Reaction`](@ref) from `substrates` and `products`.
-An equivalent alternative is `→`.
"""
-function ⟶(
+function →(
substrates::Union{
Nothing,
Metabolite,
@@ -97,10 +96,9 @@ function ⟶(
metdict = _mkrxn(substrates, products)
return Reaction("", metdict, :forward)
end
-const → = ⟶
"""
- ⟵(
+ â†(
substrates::Union{
Nothing,
Metabolite,
@@ -116,9 +114,8 @@ const → = ⟶
)
Make a reverse-only [`Reaction`](@ref) from `substrates` and `products`.
-An equivalent alternative is `â†`.
"""
-function ⟵(
+function â†(
substrates::Union{
Nothing,
Metabolite,
@@ -135,10 +132,9 @@ function ⟵(
metdict = _mkrxn(substrates, products)
return Reaction("", metdict, :reverse)
end
-const ↠= ⟵
"""
- ⟷(
+ ↔(
substrates::Union{
Nothing,
Metabolite,
@@ -153,10 +149,10 @@ const ↠= ⟵
},
)
-Make a bidirectional (reversible) [`Reaction`](@ref) from `substrates` and `products`.
-An equivalent alternative is `↔`.
+Make a bidirectional (reversible) [`Reaction`](@ref) from `substrates` and
+`products`.
"""
-function ⟷(
+function ↔(
substrates::Union{
Nothing,
Metabolite,
@@ -173,4 +169,3 @@ function ⟷(
metdict = _mkrxn(substrates, products)
return Reaction("", metdict, :bidirectional)
end
-const ↔ = ⟷
diff --git a/src/reconstruction/StandardModel.jl b/src/reconstruction/StandardModel.jl
index cc7b2d2a8109f4f9e1184c227f2961f6b5b86273..da0f85eb9e0448534ed06fccd0dea25999304256 100644
--- a/src/reconstruction/StandardModel.jl
+++ b/src/reconstruction/StandardModel.jl
@@ -77,9 +77,9 @@ Examples
--------
```
@add_reactions! model begin
- "v1", nothing ⟶ A, 0, 500
- "v2", A ⟷ B + C, -500
- "v3", B + C ⟶ nothing
+ "v1", nothing → A, 0, 500
+ "v2", A ↔ B + C, -500
+ "v3", B + C → nothing
end
```
"""
diff --git a/test/reconstruction/CoreModel.jl b/test/reconstruction/CoreModel.jl
index b63ce8745a62a1668d84850a2ff5f9d0265ec69c..ac704b6ff6534bf446c7ad18dc25d27a49426b46 100644
--- a/test/reconstruction/CoreModel.jl
+++ b/test/reconstruction/CoreModel.jl
@@ -231,8 +231,8 @@ end
@test size(stoichiometry(m2)) == (71, 94)
@test size(stoichiometry(m3)) == (70, 94)
@test size(stoichiometry(m4)) == (71, 94)
- @test any(["glc__D_e", "for_c"] .∉ Ref(metabolites(m1)))
- @test any(["glc__D_e"] .∉ Ref(metabolites(m2)))
- @test any(["glc__D_e", "for_c"] .∉ Ref(metabolites(m3)))
- @test any(["glc__D_e"] .∉ Ref(metabolites(m4)))
+ @test all((!in(metabolites(m1))).(["glc__D_e", "for_c"]))
+ @test !(["glc__D_e"] in metabolites(m2))
+ @test all((!in(metabolites(m3))).(["glc__D_e", "for_c"]))
+ @test !(["glc__D_e"] in metabolites(m4))
end
diff --git a/test/reconstruction/Reaction.jl b/test/reconstruction/Reaction.jl
index 5b5340f176dded31186d2dadcdfed79b5d9a30ba..aa0c84812f410aced42d256b3e380e028350dfed 100644
--- a/test/reconstruction/Reaction.jl
+++ b/test/reconstruction/Reaction.jl
@@ -9,7 +9,7 @@
nad = model.metabolites["nad_c"]
h_p = model.metabolites["h_p"]
- rxn = nadh + 4.0 * h_c + 1.0 * q8 ⟶ 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
+ rxn = nadh + 4.0 * h_c + 1.0 * q8 → 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
@test rxn.lb == 0.0 && rxn.ub > 0.0
rxn = 1.0 * nadh + 4.0 * h_c + q8 ↠1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
@@ -27,11 +27,11 @@
rxn = nothing → 1.0nadh
@test length(rxn.metabolites) == 1
- rxn = 1.0 * nadh + 4.0 * h_c + 1.0 * q8 ⟶ 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
+ rxn = 1.0 * nadh + 4.0 * h_c + 1.0 * q8 → 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
@test prod(values(rxn.metabolites)) == -12
@test ("q8h2_c" in [x for x in keys(rxn.metabolites)])
- rxn = nadh + 4.0 * h_c + 1.0 * q8 ⟶ 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
+ rxn = nadh + 4.0 * h_c + 1.0 * q8 → 1.0 * q8h2 + 1.0 * nad + 3.0 * h_p
@test rxn.lb == 0.0 && rxn.ub > 0.0
@test length(h_p + h_p) == 2
diff --git a/test/reconstruction/add_reactions.jl b/test/reconstruction/add_reactions.jl
index 4c452cc0a9a5cf8ae10026c02e5653375a8b8fb7..823432f37ad758c050ab229a4ad23846ae2f5774 100644
--- a/test/reconstruction/add_reactions.jl
+++ b/test/reconstruction/add_reactions.jl
@@ -6,9 +6,9 @@
add_metabolites!(mod, [A, B, C])
@add_reactions! mod begin
- "v1", nothing ⟷ A
- "v2", nothing ⟷ B, -500
- "v3", nothing ⟷ C, -500, 500
+ "v1", nothing ↔ A
+ "v2", nothing ↔ B, -500
+ "v3", nothing ↔ C, -500, 500
end
rxn = mod.reactions["v1"]