Check for validity of molecules when reading

[cisert]

When an invalid input file is provided, OpenBabel does print a warning, but we try to keep going and return somewhat confusing errors.

• example_file_1.sdf returns Molecules at position [0] have no 3D conformations available. Either provide a mol with one or re-run calculator with force3D=True.
• example_file_2.sdf returns need at least one array to concatenate

example_files.zip

Checking if molecules are valid and throwing an error if not might be clearer for the user. In the two cases above, input_ is either a list of empty (no atoms) pybel molecules (for example_file_1.sdf) or just an empty list (for example_file_2.sdf), so we could check for that.