Move to 1-indexing for PDB/CIFs

[jakublala]

This will require some work on the boileroom end as well -- but it will be more consistent with how other packages work and what is the general convention.

We will need to carefully make sure that nothing is broken by this -- as it was a problem when we moved to 1-indexing before, @arnav-cheruku remembers.

[jakublala]

Related to softnanolab/boileroom#31

[jakublala]

The way that one selects hotspots should be potentially done with some string interface that makes it clear that one needs the 1-indexing, as otherwise the List[Residue] is effectively 0-indexed, because it is a Python list.