Just a quick heads up, the update to version 3.0 breaks the API in a number of cases, and introduces some new behaviour behind-the-scenes.

For full details https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html.

In particular

The babel executable has been removed, and obabel should be used instead.

In OB 3.x, both openbabel.py and pybel.py live within the openbabel module

There are also changes to the handling of elements, atoms and bond flags, and aromaticity.