> My second question is regarding running python programs in command line,
> have you ever tried to run the python program that imports pybel from inside
> a batch file? For me this throws an error "ModuleNotFoundError: No module
> named pybel".

One way or another, the environment is different. While you mention including 
the Pybel and openbabel.py files in the site-packages directory, my guess is 
that they're not being loaded somehow.

Since there aren't a whole lot of Windows users on here, I'm afraid we can't be 
much help. But you're doing the right thing - checking that things run from the 
command-line first. Somehow, the environment of the batch file is different 
than the command-line.

-Geoff

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