API

BNGNetwork()

File-format selector for BioNetGen .net reaction network files.

Arguments

None.

Keywords

None.

Fields

None.

Pass BNGNetwork() to loadrxnetwork to parse a BioNetGen .net file into a Catalyst ReactionSystem.

Examples

using ReactionNetworkImporters

BNGNetwork() isa ReactionNetworkImporters.NetworkFileFormat

# output
true

MatrixNetwork(rateexprs, substoich, prodstoich; species = Any[], params = Any[], t = nothing)

Input representation for constructing a Catalyst reaction network from substrate and product stoichiometry matrices.

Arguments

• rateexprs::AbstractVector: One symbolic or numeric rate expression per reaction.
• substoich::AbstractMatrix: Species-by-reaction substrate coefficients.
• prodstoich::AbstractMatrix{Int}: Species-by-reaction product coefficients; it must have the same size as substoich.

Keywords

• species::AbstractVector = Any[]: Symbolic species in row order. Empty uses generated species with the chosen independent variable.
• params::AbstractVector = Any[]: Symbolic parameters referenced by rateexprs.
• t = nothing: Independent variable. nothing uses Catalyst.default_t().

Fields

• rateexprs: Rate expressions, one for each reaction column.
• substoich: Substrate stoichiometry matrix.
• prodstoich: Product stoichiometry matrix.
• species: Symbolic species in matrix-row order.
• params: Symbolic parameters available to rate expressions.
• t: Independent variable or nothing.

Examples

using ReactionNetworkImporters

network = MatrixNetwork([1.0], reshape([1], 1, 1), reshape([0], 1, 1))
network isa MatrixNetwork

# output
true

ComplexMatrixNetwork(rateexprs, stoichmat, incidencemat; species = Any[], params = Any[], t = nothing)

Input representation for constructing a Catalyst reaction network from complex stoichiometry and complex-incidence matrices.

Arguments

• rateexprs::AbstractVector: One symbolic or numeric rate expression per reaction.
• stoichmat::AbstractMatrix: Species-by-complex nonnegative stoichiometric coefficients.
• incidencemat::AbstractMatrix{Int}: Complex-by-reaction matrix whose entries are -1, 0, or 1.

Keywords

• species::AbstractVector = Any[]: Symbolic species in row order. Empty uses generated species with the chosen independent variable.
• params::AbstractVector = Any[]: Symbolic parameters referenced by rateexprs.
• t = nothing: Independent variable. nothing uses Catalyst.default_t().

Fields

• rateexprs: Rate expressions, one for each reaction column.
• stoichmat: Species-by-complex stoichiometry matrix.
• incidencemat: Complex-by-reaction incidence matrix.
• species: Symbolic species in matrix-row order.
• params: Symbolic parameters available to rate expressions.
• t: Independent variable or nothing.

Examples

using ReactionNetworkImporters

network = ComplexMatrixNetwork([1.0], [1 0], reshape([-1, 1], 2, 1))
network isa ComplexMatrixNetwork

# output
true

loadrxnetwork(ft::BNGNetwork, rxfilename; name = gensym(:ReactionSystem), verbose = true, kwargs...)

Parse a BioNetGen .net file and construct a Catalyst ReactionSystem.

Arguments

• ft::BNGNetwork: Selector for the BioNetGen .net format.
• rxfilename::AbstractString: Path to the network file.

Keywords

• name::Symbol = gensym(:ReactionSystem): Name assigned to the returned system.
• verbose::Bool = true: Print parser progress when true.
• kwargs...: Additional keywords forwarded to ReactionSystem.

Returns

• ReactionSystem: Incomplete Catalyst system. Its metadata contains initial conditions, parameter values, BNG variable names, and BNG group observables.

Rules

• Supports parameter expressions, fixed species, compartment-prefixed species, elementary and Sat rate laws, function blocks, and groups.
• MM, Hill, and tfun() constructs are unsupported and throw an error.
• Call complete on the returned system before constructing a SciML problem.

Examples

using ReactionNetworkImporters

format = BNGNetwork()
format isa ReactionNetworkImporters.NetworkFileFormat

# output
true

loadrxnetwork(mn::MatrixNetwork; name = gensym(:ReactionSystem))

Convert a MatrixNetwork into a Catalyst ReactionSystem.

Arguments

• mn::MatrixNetwork: Input matrix representation satisfying MatrixNetwork's dimensionality rules.

Keywords

• name::Symbol = gensym(:ReactionSystem): Name assigned to the resulting system.

Returns

• ReactionSystem: An incomplete Catalyst system. Call complete before using it to construct a SciML problem.

Rules

• substoich and prodstoich must be species-by-reaction matrices of equal size.
• Each rate expression corresponds to one reaction column.
• An empty species vector requests generated species symbols.

Examples

using ReactionNetworkImporters

network = MatrixNetwork([1.0], reshape([1], 1, 1), reshape([0], 1, 1))
system = loadrxnetwork(network; name = :decay)
nameof(system)

# output
:decay

loadrxnetwork(cmn::ComplexMatrixNetwork; name = gensym(:ReactionSystem))

Convert a ComplexMatrixNetwork into a Catalyst ReactionSystem.

Arguments

• cmn::ComplexMatrixNetwork: Complex-matrix representation satisfying the documented stoichiometry and incidence rules.

Keywords

• name::Symbol = gensym(:ReactionSystem): Name assigned to the resulting system.

Returns

• ReactionSystem: An incomplete Catalyst system. Call complete before using it to construct a SciML problem.

Rules

• stoichmat is species-by-complex and has nonnegative entries.
• incidencemat is complex-by-reaction with entries in (-1, 0, 1).
• Every reaction column needs one substrate complex (-1) and one product complex (1).

Examples

using ReactionNetworkImporters

network = ComplexMatrixNetwork([1.0], [1 0], reshape([-1, 1], 2, 1))
system = loadrxnetwork(network; name = :conversion)
nameof(system)

# output
:conversion

VarsToNames

Metadata key for storing BNG variable-to-full-name mappings on a ReactionSystem. Stores a Dict mapping internal symbolic variables (both dynamic species and constant-species parameters) to their full BNG name strings from the .net file.

Fields

None. This fieldless type is used as a metadata key.

See also: has_varstonames, get_varstonames, set_varstonames

GroupsToSyms

Metadata key for storing BNG group-name-to-symbol mappings on a ReactionSystem. Stores a Dict mapping String group names to corresponding symbolic observable variables.

Fields

None. This fieldless type is used as a metadata key.

See also: has_groupstosyms, get_groupstosyms, set_groupstosyms

has_varstonames(rs::ReactionSystem)

Return whether rs has a VarsToNames metadata entry.

Arguments

• rs::ReactionSystem: System to inspect.

Returns

• Bool: true when the mapping exists.

get_varstonames(rs::ReactionSystem)

Return the VarsToNames mapping from rs, or nothing when it is absent.

Arguments

• rs::ReactionSystem: System to inspect.

Returns

• Dict or nothing: Mapping from system variables to BioNetGen names.

set_varstonames(rs::ReactionSystem, m)

Return a new ReactionSystem with the VarsToNames metadata set to m.

Arguments

• rs::ReactionSystem: System to update.
• m: Mapping from system variables to BioNetGen names.

Returns

• ReactionSystem: Copy of rs carrying m; rs is not mutated.

has_groupstosyms(rs::ReactionSystem)

Return whether rs has a GroupsToSyms metadata entry.

Arguments

• rs::ReactionSystem: System to inspect.

Returns

• Bool: true when the mapping exists.

get_groupstosyms(rs::ReactionSystem)

Return the GroupsToSyms mapping from rs, or nothing when it is absent.

Arguments

• rs::ReactionSystem: System to inspect.

Returns

• Dict or nothing: Mapping from BioNetGen group names to observables.

set_groupstosyms(rs::ReactionSystem, m)

Return a new ReactionSystem with the GroupsToSyms metadata set to m.

Arguments

• rs::ReactionSystem: System to update.
• m: Mapping from BioNetGen group names to observables.

Returns

• ReactionSystem: Copy of rs carrying m; rs is not mutated.