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@TorkelE
TorkelE committed Jul 14, 2024
1 parent d0400a2 commit 4603532
Showing 1 changed file with 40 additions and 38 deletions.
78 changes: 40 additions & 38 deletions src/network_analysis.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
function filter_constspecs(specs, stoich::AbstractVector{V}, smap) where {V <: Integer}
isempty(specs) && (return Vector{Int}(), Vector{V}())

# If any species are constant, go through these manually and add their indices and
# stoichiometries to `ids` and `filtered_stoich`.
# if any species are constant, go through these manually and add their indices and
# stoichiometries to `ids` and `filtered_stoich`
if any(isconstant, specs)
ids = Vector{Int}()
filtered_stoich = Vector{V}()
Expand Down Expand Up @@ -46,15 +46,15 @@ function reactioncomplexmap(rn::ReactionSystem)
!isempty(nps.complextorxsmap) && return nps.complextorxsmap
complextorxsmap = nps.complextorxsmap

# Retrieves system reactions and a map from species to their index in the species vector.
# retrieves system reactions and a map from species to their index in the species vector
rxs = reactions(rn)
smap = speciesmap(rn)
numreactions(rn) > 0 ||
error("There must be at least one reaction to find reaction complexes.")

for (i, rx) in enumerate(rxs)
# Create the `ReactionComplex` corresponding to the reaction's substrates. Adds it
# to the reaction complex dictionary (recording it as the substrates of the i'th reaction).
# to the reaction complex dictionary (recording it as the substrates of the i'th reaction).
subids, substoich = filter_constspecs(rx.substrates, rx.substoich, smap)
subrc = sort!(ReactionComplex(subids, substoich))
if haskey(complextorxsmap, subrc)
Expand All @@ -64,7 +64,7 @@ function reactioncomplexmap(rn::ReactionSystem)
end

# Create the `ReactionComplex` corresponding to the reaction's products. Adds it
# to the reaction complex dictionary (recording it as the products of the i'th reaction).
# to the reaction complex dictionary (recording it as the products of the i'th reaction).
prodids, prodstoich = filter_constspecs(rx.products, rx.prodstoich, smap)
prodrc = sort!(ReactionComplex(prodids, prodstoich))
if haskey(complextorxsmap, prodrc)
Expand Down Expand Up @@ -103,7 +103,7 @@ function reactioncomplexes(rn::ReactionSystem; sparse = false)
error("reactioncomplexes does not currently support subsystems.")
nps = get_networkproperties(rn)

# If the complexes have not been cached, or the cached complexes uses a different sparsity.
# if the complexes have not been cached, or the cached complexes uses a different sparsity
if isempty(nps.complexes) || (sparse != issparse(nps.complexes))
# Computes the reaction complex dictionary. Use it to create a sparse/dense matrix.
complextorxsmap = reactioncomplexmap(rn)
Expand All @@ -116,11 +116,11 @@ function reactioncomplexes(rn::ReactionSystem; sparse = false)
nps.complexes, nps.incidencemat
end

# Creates a *sparse* reaction complex matrix.
# creates a *sparse* reaction complex matrix
function reactioncomplexes(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSystem,
complextorxsmap)
# Computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information).
# computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information)
complexes = collect(keys(complextorxsmap))
Is = Int[]
Js = Int[]
Expand All @@ -136,7 +136,7 @@ function reactioncomplexes(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSystem
complexes, B
end

# Creates a *dense* reaction complex matrix.
# creates a *dense* reaction complex matrix
function reactioncomplexes(::Type{Matrix{Int}}, rn::ReactionSystem, complextorxsmap)
complexes = collect(keys(complextorxsmap))
B = zeros(Int, length(complexes), numreactions(rn))
Expand Down Expand Up @@ -174,8 +174,8 @@ function complexstoichmat(rn::ReactionSystem; sparse = false)
error("complexstoichmat does not currently support subsystems.")
nps = get_networkproperties(rn)

# If the complexes stoichiometry matrix has not been cached, or the cached one uses a
# different sparsity, computes (and caches) it.
# if the complexes stoichiometry matrix has not been cached, or the cached one uses a
# different sparsity, computes (and caches) it
if isempty(nps.complexstoichmat) || (sparse != issparse(nps.complexstoichmat))
nps.complexstoichmat = if sparse
complexstoichmat(SparseMatrixCSC{Int, Int}, rn, keys(reactioncomplexmap(rn)))
Expand All @@ -186,10 +186,10 @@ function complexstoichmat(rn::ReactionSystem; sparse = false)
nps.complexstoichmat
end

# Creates a *sparse* reaction complex stoichiometry matrix.
# creates a *sparse* reaction complex stoichiometry matrix
function complexstoichmat(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSystem, rcs)
# Computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information).
# computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information)
Is = Int[]
Js = Int[]
Vs = Int[]
Expand All @@ -203,7 +203,7 @@ function complexstoichmat(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSystem,
Z = sparse(Is, Js, Vs, numspecies(rn), length(rcs))
end

# Creates a *dense* reaction complex stoichiometry matrix.
# creates a *dense* reaction complex stoichiometry matrix
function complexstoichmat(::Type{Matrix{Int}}, rn::ReactionSystem, rcs)
Z = zeros(Int, numspecies(rn), length(rcs))
for (i, rc) in enumerate(rcs)
Expand Down Expand Up @@ -236,8 +236,8 @@ function complexoutgoingmat(rn::ReactionSystem; sparse = false)
error("complexoutgoingmat does not currently support subsystems.")
nps = get_networkproperties(rn)

# If the outgoing complexes matrix has not been cached, or the cached one uses a
# different sparsity, computes (and caches) it.
# if the outgoing complexes matrix has not been cached, or the cached one uses a
# different sparsity, computes (and caches) it
if isempty(nps.complexoutgoingmat) || (sparse != issparse(nps.complexoutgoingmat))
B = reactioncomplexes(rn, sparse = sparse)[2]
nps.complexoutgoingmat = if sparse
Expand All @@ -249,18 +249,18 @@ function complexoutgoingmat(rn::ReactionSystem; sparse = false)
nps.complexoutgoingmat
end

# Creates a *sparse* outgoing reaction complex stoichiometry matrix.
# creates a *sparse* outgoing reaction complex stoichiometry matrix
function complexoutgoingmat(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSystem, B)
# Computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information).
# computes the I, J, and V vectors used for the sparse matrix (read about sparse matrix
# representation for more information)
n = size(B, 2)
rows = rowvals(B)
vals = nonzeros(B)
Is = Int[]
Js = Int[]
Vs = Int[]

# Allocates space to the vectors (so that it is not done incrementally in the loop).
# allocates space to the vectors (so that it is not done incrementally in the loop)
sizehint!(Is, div(length(vals), 2))
sizehint!(Js, div(length(vals), 2))
sizehint!(Vs, div(length(vals), 2))
Expand All @@ -277,7 +277,7 @@ function complexoutgoingmat(::Type{SparseMatrixCSC{Int, Int}}, rn::ReactionSyste
sparse(Is, Js, Vs, size(B, 1), size(B, 2))
end

# Creates a *dense* outgoing reaction complex stoichiometry matrix.
# creates a *dense* outgoing reaction complex stoichiometry matrix
function complexoutgoingmat(::Type{Matrix{Int}}, rn::ReactionSystem, B)
Δ = copy(B)
for (I, b) in pairs(Δ)
Expand Down Expand Up @@ -310,7 +310,7 @@ function incidencematgraph(rn::ReactionSystem)
nps.incidencegraph
end

# Computes the incidence graph from an *dense* incidence matrix.
# computes the incidence graph from an *dense* incidence matrix
function incidencematgraph(incidencemat::Matrix{Int})
@assert all(∈([-1, 0, 1]), incidencemat)
n = size(incidencemat, 1) # no. of nodes/complexes
Expand All @@ -331,7 +331,7 @@ function incidencematgraph(incidencemat::Matrix{Int})
return graph
end

# Computes the incidence graph from an *sparse* incidence matrix.
# computes the incidence graph from an *sparse* incidence matrix
function incidencematgraph(incidencemat::SparseMatrixCSC{Int, Int})
@assert all(∈([-1, 0, 1]), incidencemat)
m, n = size(incidencemat)
Expand Down Expand Up @@ -420,16 +420,18 @@ function terminallinkageclasses(rn::ReactionSystem)
nps.terminallinkageclasses
end

# Helper function for terminallinkageclasses. Given a linkage class and a reaction network, say whether the linkage class is terminal,
# i.e. all outgoing reactions from complexes in the linkage class produce a complex also in the linkage class
# Helper function for terminallinkageclasses. Given a linkage class and a reaction network, say
# whether the linkage class is terminal, i.e. all outgoing reactions from complexes in the linkage
# class produce a complex also in the linkage class
function isterminal(lc::Vector, rn::ReactionSystem)
imat = incidencemat(rn)

for r in 1:size(imat, 2)
# Find the index of the reactant complex for a given reaction
s = findfirst(==(-1), @view imat[:, r])

# If the reactant complex is in the linkage class, check whether the product complex is also in the linkage class. If any of them are not, return false.
# If the reactant complex is in the linkage class, check whether the product complex is
# also in the linkage class. If any of them are not, return false.
if s in Set(lc)
p = findfirst(==(1), @view imat[:, r])
p in Set(lc) ? continue : return false
Expand Down Expand Up @@ -697,7 +699,7 @@ conservation laws, each represented as a row in the output.
function conservationlaws(nsm::T; col_order = nothing) where {T <: AbstractMatrix}

# compute the left nullspace over the integers
# The `nullspace` function updates the `col_order`.
# the `nullspace` function updates the `col_order`
N = MT.nullspace(nsm'; col_order)

# if all coefficients for a conservation law are negative, make positive
Expand All @@ -713,7 +715,7 @@ function conservationlaws(nsm::T; col_order = nothing) where {T <: AbstractMatri
T(N')
end

# Used in the subsequent function.
# used in the subsequent function
function cache_conservationlaw_eqs!(rn::ReactionSystem, N::AbstractMatrix, col_order)
# Retrieves nullity (the number of conservation laws). `r` is the rank of the netstoichmat.
nullity = size(N, 1)
Expand All @@ -728,7 +730,7 @@ function cache_conservationlaw_eqs!(rn::ReactionSystem, N::AbstractMatrix, col_o
depidxs = col_order[(r + 1):end]
depspecs = sps[depidxs]

# Declares the conservation law parameters.
# declares the conservation law parameters
constants = MT.unwrap.(MT.scalarize(only(
@parameters $(CONSERVED_CONSTANT_SYMBOL)[1:nullity] [conserved = true])))

Expand All @@ -738,20 +740,20 @@ function cache_conservationlaw_eqs!(rn::ReactionSystem, N::AbstractMatrix, col_o
conservedeqs = Equation[]
constantdefs = Equation[]

# For each conserved quantity.
# for each conserved quantity
for (i, depidx) in enumerate(depidxs)
# Finds the coefficient (in the conservation law) of the species that is eliminated
# by this conservation law.
# finds the coefficient (in the conservation law) of the species that is eliminated
# by this conservation law
scaleby = (N[i, depidx] != 1) ? N[i, depidx] : one(eltype(N))
(scaleby != 0) || error("Error, found a zero in the conservation law matrix where "
* "one was not expected.")

# Creates, for this conservation law, the sum of all independent species (weighted by
# the ratio between the coefficient of the species and the species which is elimianted.
# creates, for this conservation law, the sum of all independent species (weighted by
# the ratio between the coefficient of the species and the species which is elimianted
coefs = @view N[i, indepidxs]
terms = sum(coef / scaleby * sp for (coef, sp) in zip(coefs, indepspecs))

# Computes the two equations corresponding to this conserved quantity.
# computes the two equations corresponding to this conserved quantity
eq = depspecs[i] ~ constants[i] - terms
push!(conservedeqs, eq)
eq = constants[i] ~ depspecs[i] + terms
Expand Down Expand Up @@ -784,7 +786,7 @@ function conservationlaws(rs::ReactionSystem)
nps = get_networkproperties(rs)
!isempty(nps.conservationmat) && (return nps.conservationmat)

# If the conservation law matrix is not computed, do so and caches the result.
# if the conservation law matrix is not computed, do so and caches the result
nsm = netstoichmat(rs)
nps.conservationmat = conservationlaws(nsm; col_order = nps.col_order)
cache_conservationlaw_eqs!(rs, nps.conservationmat, nps.col_order)
Expand Down

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