Is there an algorithm that counts Joback groups in a structure?
So it looks like 'Jobeck groups' are some set of functional groups that you want to find in molecules.

Sounds a lot like substructure search, for which there are many cheminformatics tools (like SMSD, for example) however, since you mention OpenBabel:

http://open-babel.readthedocs.org/en/latest/WritePlugins/AddNewDescriptor.html

talks specifically about 'group contribution methods' and gives a simple example of how to get the counts for a set of functional groups.