Is your feature request related to a problem?

modernize HBA (HydrogenBondAnalysis) to use AG (AtomGroups) as objects internally instead of selection strings to avoid the need for HBA analysis to discern the relevant atoms.

Describe the solution you'd like

AG as objects internally instead of selection strings

Additional context

See PR Hbond update #3848 (in particular #3848 (comment))

Guidance for new contributors

This is a reasonably complicated issue to solve for a beginner. We recommend you first learn about the problem. Ask questions here. The more specific your question, then better we can help.

As the first steps you should:

• Familiarize yourself with AtomGroups and UpdatingAtomGroups. Understand the difference between the two.
• Understand the difference between using selection strings to describe groups of atoms and using AtomGroups for the same purpose.
• Read the code for HydrogenBondAnalysis in package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py. Be able to identify the pieces of code that use selection strings.

EDITS

• made issue clearer for new contributors (@orbeckst )