Commit 939d677b authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

efficient building of JSONModel stoichiometry

parent f20e41f1
...@@ -107,22 +107,36 @@ function stoichiometry(model::JSONModel) ...@@ -107,22 +107,36 @@ function stoichiometry(model::JSONModel)
rxn_ids = reactions(model) rxn_ids = reactions(model)
met_ids = metabolites(model) met_ids = metabolites(model)
S = SparseArrays.spzeros(length(met_ids), length(rxn_ids)) n_entries = 0
for r in model.rxns
for _ in r["metabolites"]
n_entries += 1
MI = Vector{Int}()
RI = Vector{Int}()
SV = Vector{Float64}()
sizehint!(MI, n_entries)
sizehint!(RI, n_entries)
sizehint!(SV, n_entries)
for (i, rid) in enumerate(rxn_ids) for (i, rid) in enumerate(rxn_ids)
r = model.rxns[model.rxn_index[rid]] r = model.rxns[model.rxn_index[rid]]
for (mid, coeff) in r["metabolites"] for (mid, coeff) in r["metabolites"]
if !haskey(model.met_index, mid) haskey(model.met_index, mid) || throw(
throw( DomainError(
DomainError( met_id,
met_id, "Unknown metabolite found in stoichiometry of $(rxn_ids[i])",
"Unknown metabolite found in stoichiometry of $(rxn_ids[i])", ),
), )
end push!(MI, model.met_index[mid])
S[model.met_index[mid], i] = coeff push!(RI, i)
push!(SV, coeff)
end end
end end
return S return SparseArrays.sparse(MI, RI, SV, length(met_ids), length(rxn_ids))
end end
""" """
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