cobra¶

cobrapy based helper methods.

cobrapy is not a dependency of sbmlutils, it is the optional cobra extra (pip install sbmlutils[cobra]). cobra is None when it is not installed, which is what the tests of this module skip on.

read_cobra_model ¶

read_cobra_model(sbml_path)

Load cobra model from path.

Sets default flux bounds to allow loading and changes all boundaryConditions to False.

:param sbml_path: str path :return: cobra model

cobra_reaction_info ¶

cobra_reaction_info(cobra_model)

Create data frame with bound and objective information.

:param cobra_model: :return: pandas DataFrame

check_mass_balance ¶

check_mass_balance(sbml_path)

Check mass and charge balance of the model.

Parameters:

Name	Type	Description	Default
`sbml_path`	`Path`	path of the SBML model	required

Returns:

Type	Description
`dict[str, Any]`	The unbalanced reactions, keyed by reaction id.