SBML

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

Core SBML

annnet.io.sbml

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 (Systems Biology Markup Language) → AnnNet adapter

---

Targets the provided AnnNet API.

Two entry points: - from_sbml(path, graph=None, slice="default", preserve_stoichiometry=True) - from_cobra_model(model, graph=None, slice="default", preserve_stoichiometry=True)

If AnnNet.set_edge_coeffs(edge_id, coeffs: dict[str, float]) is not available, stoichiometric coefficients are stored under an edge attribute stoich (lossy but usable).

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; falls back to python-libsbml (if you extend this file).