Refactor `align_full` in `libnotebooks`

[AnnaKravchenko]

As indicated via FIXME in libnotebooks.py:

1. align_full shoukd be splitted into several smaller and (thus) more manageable functions;
2. Doscstricng placeholders should be replaces with actual funciont descriptions for all function;
3. Functions load_pdb_file, pdb_string_to_structure and structure_to_pdb_string should have type hints.