Path finding

This module implements finding paths in a BioPaxModel starting from a given object using a path constraint string.

exception pybiopax.paths.BiopaxClassConstraintError(cls_str)

Bases: KeyError

pybiopax.paths.find_objects(start_obj, path_str)

Return objects matching the given path specification.

Parameters

• start_obj (BioPaxObject) – The object to start the search from.

• path_str (str) – A path specification string which consists of one or more parts separated by /. Each part is the name of an object attribute, and can optionally contain a class name as well, separated by : to constrain the class of the target of the attribute to consider. Optionally, each attribute can also have a * suffix to make the search recursive.

Return type

List[BioPaxObject]

Returns

A list of BioPaxObjects satisfying the given path specification.