Generic accessors

To prevent the complexities of object representation, COBREXA.jl uses a set of generic interface functions that can extract various important information from any supported model type. This approach ensures that the analysis functions can work on any data.

For example, you can check the reactions and metabolites contained in any model type (SBMLModel, JSONModel, CoreModel, StandardModel, and any other) using the same accessor:

using COBREXA

!isfile("e_coli_core.json") &&
    download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json");

js = load_model("e_coli_core.json")
reactions(js)

95-element Vector{String}:
 "PFK"
 "PFL"
 "PGI"
 "PGK"
 "PGL"
 "ACALD"
 "AKGt2r"
 "PGM"
 "PIt2r"
 "ALCD2x"
 ⋮
 "MALt2_2"
 "MDH"
 "ME1"
 "ME2"
 "NADH16"
 "NADTRHD"
 "NH4t"
 "O2t"
 "PDH"

std = convert(CoreModel, js)
reactions(std)

95-element Vector{String}:
 "PFK"
 "PFL"
 "PGI"
 "PGK"
 "PGL"
 "ACALD"
 "AKGt2r"
 "PGM"
 "PIt2r"
 "ALCD2x"
 ⋮
 "MALt2_2"
 "MDH"
 "ME1"
 "ME2"
 "NADH16"
 "NADTRHD"
 "NH4t"
 "O2t"
 "PDH"

All accessors allow systematic access to information about reactions, stoichiometry, metabolite properties and chemistry, genes, and various model annotations.

The most notable ones include:

reactions, metabolites and genes return respective vectors of identifiers of reactions, metabolites and genes present in the model,
stoichiometry returns the S matrix
balance returns the right-hand vector of the linear model in form Ax=b
bounds return lower and upper bounds of reaction rates
metabolite_charge and metabolite_formula return details about metabolites
objective returns the objective of the model (usually labeled as c)
reaction_gene_association describes the dependency of a reaction on gene products

A complete, up-to-date list of accessors can be always generated using methodswith:

using InteractiveUtils

accessors = [
    x.name for x in methodswith(MetabolicModel, COBREXA) if
    endswith(String(x.file), "MetabolicModel.jl")
]

println.(accessors);

balance
bounds
coupling
coupling_bounds
fluxes
gene_annotations
gene_name
gene_notes
genes
metabolite_annotations
metabolite_charge
metabolite_compartment
metabolite_formula
metabolite_name
metabolite_notes
metabolites
n_coupling_constraints
n_fluxes
n_genes
n_metabolites
n_reactions
objective
precache!
reaction_annotations
reaction_flux
reaction_gene_association
reaction_name
reaction_notes
reaction_stoichiometry
reaction_subsystem
reactions
stoichiometry

Note: Not all accessors may be implemented for all the models

It is possible that not all the accessors are implemented for all the model types. If this is the case, usually nothing or an empty data structure is returned. If you need a specific accessor, just overload the function you require!

This page was generated using Literate.jl.