API

convert_simplify_math(args...)

Compatibility alias for SBML.convert_promotelocals_expandfuns.

All arguments are forwarded unchanged. New code should import and call SBML.convert_promotelocals_expandfuns directly.

Examples

normalized_document = convert_simplify_math(document)

ReactionSystem(model::SBML.Model; kwargs...)

Convert an SBML.Model to a completed Catalyst.ReactionSystem.

Arguments

• model::SBML.Model: the normalized SBML model to convert.

Keywords

• kwargs...: forwarded to Catalyst.ReactionSystem.

Returns

• Catalyst.ReactionSystem: the completed reaction system.

Examples

model = readSBML("model.xml", DefaultImporter())
reaction_system = ReactionSystem(model)

ODESystem(model::SBML.Model; include_zero_odes = true, kwargs...)

Convert an SBML.Model to a completed ModelingToolkit.ODESystem.

Arguments

• model::SBML.Model: the normalized SBML model to convert.

Keywords

• include_zero_odes::Bool = true: retain equations with zero right-hand sides.
• kwargs...: forwarded while constructing the intermediate reaction system.

Returns

• ModelingToolkit.ODESystem: the completed ODE system.

Examples

model = readSBML("model.xml", DefaultImporter())
ode_system = ODESystem(model)

DefaultImporter()

Select SBMLToolkit's default normalization pipeline for SBML.readSBML.

The pipeline checks for unsupported features, upgrades the document to SBML Level 3 Version 2, and promotes local parameters and function definitions.

Examples

model = readSBML("model.xml", DefaultImporter())

ODESystemImporter()

Select conversion of an SBML file to a completed ModelingToolkit.ODESystem.

Examples

ode_system = readSBML("model.xml", ODESystemImporter())

ReactionSystemImporter()

Select conversion of an SBML file to a completed Catalyst.ReactionSystem.

Examples

reaction_system = readSBML("model.xml", ReactionSystemImporter())

readSBML(sbmlfile::String, ::DefaultImporter) -> SBML.Model

Import and normalize an SBML file for conversion to SciML system types.

Arguments

• sbmlfile::String: path to the SBML XML file.
• ::DefaultImporter: selects SBMLToolkit's default normalization pipeline.

Returns

• SBML.Model: the normalized SBML model.

Throws

• ErrorException: the file uses an unsupported SBML feature.

Examples

model = readSBML("model.xml", DefaultImporter())

readSBML(sbmlfile::String, ::ODESystemImporter; include_zero_odes = true, kwargs...)

Import an SBML file as a completed ModelingToolkit.ODESystem.

Arguments

• sbmlfile::String: path to the SBML XML file.
• ::ODESystemImporter: selects ODE-system conversion.

Keywords

• include_zero_odes::Bool = true: retain equations with zero right-hand sides.
• kwargs...: forwarded while constructing the intermediate reaction system.

Returns

• ModelingToolkit.ODESystem: the completed ODE system.

Examples

ode_system = readSBML("model.xml", ODESystemImporter())

readSBML(sbmlfile::String, ::ReactionSystemImporter; kwargs...)

Import an SBML file as a completed Catalyst.ReactionSystem.

Arguments

• sbmlfile::String: path to the SBML XML file.
• ::ReactionSystemImporter: selects reaction-system conversion.

Keywords

• kwargs...: forwarded to Catalyst.ReactionSystem.

Returns

• Catalyst.ReactionSystem: the completed reaction system.

Examples

reaction_system = readSBML("model.xml", ReactionSystemImporter())

checksupport_file(filename::String)

Validate that an SBML file uses features supported by SBMLToolkit.

Arguments

• filename::String: path to the SBML XML file.

Returns

• Bool: true when the file does not contain a known unsupported feature.

Throws

• ErrorException: the file uses an unsupported SBML feature.

Examples

checksupport_file("model.xml")