Mbarbry/ase improving pdb reader

Hi @askhl,

I'm finally back to work. I had a look on how to handle the occupancy value when not specified in the pdf reader. The thing is that in the tests from the previous version, it is expected that if the occupancy is not given in a line of the pdb file, then the array occupancy should not be written (see bbb36caf). Therefore, I guess it makes sense to keep the same logic.

Another matter, the python3 tests are failing due to a problem with hdf5 library. Do you get also such error when running the pipeline?

Best regards,

Marc