Provide selection API for partial alignment

[jaimergp]

Do you operate on full pdbs, or is it possible to select protein chains?

Originally posted by @AndreaVolkamer in #22 (comment)

[pipaj97]

Atomium is capable of selecting chains from a atomium.Model.
Wouldn't it be enough to just add a new argument for the cli?
For example: structuralalignment STRUCTURE1 STRUCTURE2 --method=METHOD --chain=A
This would take only the chain A of structure1 and structure2

you can save this chain as a pdb

[pipaj97]

It should also be possible to select specified ligands and residues, if we want that.

[jaimergp]

I'd rather do a more general approach, like --selection, correlative for each input structure. I need to give the syntax a thought though. We can pass the string directly to atomium selection queries or try to mimic selection languages from other libraries (mdtraj, Chimera, Amber...).