SBML

SBML-related import helpers from annnet.io.sbml and annnet.io.sbml_cobra.

Core SBML

annnet.io.sbml

SBML ingestion helper for AnnNet.

Provides: from_sbml(path, graph=None, slice="default", preserve_stoichiometry=True) -> AnnNet

This module reads SBML through python-libsbml when available and converts stoichiometric reactions into directed AnnNet hyperedges. Reactants and products are represented as edge endpoint sets, with optional stoichiometric coefficients stored on the edge.

Boundary reactions are represented using dedicated placeholder vertices.

Classes

Functions

from_sbml

from_sbml(
    path,
    graph=None,
    *,
    slice="default",
    preserve_stoichiometry=True
)

Read an SBML file into an AnnNet hypergraph.

Parameters:

Name	Type	Description	Default
path	str	Path to the .xml / .sbml file.	required
graph	AnnNet | None	Optional existing AnnNet to merge into.	None
slice	str	AnnNet slice name for default placement. Compartment-specific species will additionally appear in their compartment slice.	'default'
preserve_stoichiometry	bool	Write signed stoichiometric coefficients into the incidence matrix via set_edge_coeffs (reactants negative, products positive, modifiers -1). Default True.	True

COBRA SBML

annnet.io.sbml_cobra

SBML and COBRA model ingestion helpers for AnnNet.

Provides: from_sbml(path, graph=None, slice="default", preserve_stoichiometry=True) -> AnnNet from_cobra_model(model, graph=None, slice="default", preserve_stoichiometry=True) -> AnnNet

This module converts stoichiometric models into directed AnnNet hyperedges. Reactants and products are represented as edge endpoint sets, with optional stoichiometric coefficients stored on the edge.

Boundary reactions are represented using dedicated placeholder vertices.

Classes

Functions

from_cobra_model

from_cobra_model(
    model,
    graph=None,
    *,
    slice="default",
    preserve_stoichiometry=True
)

Convert a COBRApy model to AnnNet. Requires cobra.util.array.create_stoichiometric_matrix.

Edge attributes added: name, default_lb, default_ub, gpr (Gene-Protein-Reaction rule [GPR]).

from_sbml

from_sbml(
    path,
    graph=None,
    *,
    slice="default",
    preserve_stoichiometry=True
)

Read SBML using COBRApy if available.