Module biodivine_lib_param_bn::sbml::import

Contains code for parsing SBML models using xml-tree library. It is not 100% SBML-qual compliant, but should be good enough for now. Also most code is ready for possible extension to multi-valued models in the future.

Modules

_convert_mathml_to_fn_update

_read_layout

Used for reading SBML layout specifications.

_read_mathml

_read_species

_read_transitions

Constants

MATHML

SBML

SBML_LAYOUT

SBML_QUAL

Functions

child_tags

(internal) Find all child Nodes that have a given name.

create_explicit_parameters

(internal) Create any explicit parameters used in the given MathML tree.

create_normalized_names

(internal) Assigns every specie a biodivine-friendly name. Returns a mapping between SBML IDs and valid specie names.

create_regulations

(internal) Add regulations to a RegulatoryGraph based on the collection of SBMLTransitions.

read_unique_child

(internal) Find the given tag in a parent Node. Returns error if the tag does not exist or is present in multiple instances.