Add reference point to geometric selections

[richardjgowers]

Is your feature request related to a problem?

We currently have a bunch of selections that are select_atoms('sphzone 3.0 protein'), for a full list:

https://docs.mdanalysis.org/stable/documentation_pages/selections.html#geometric

This takes the COG of a selection to use as a reference point. Sometimes it would be nice to manually specify the reference point

Describe the solution you'd like

To select a spherical zone around point x=1.1 y=1.2 z=1.3, something like:

select_atoms('sphzone 3.0 point 1.1 1.2 1.3')

Describe alternatives you've considered

Additional context

[abdulasiraj]

Hi @richardjgowers can I start working on this?

[richardjgowers]

@abdulasiraj yep, if you think you can solve the issue then go for it!

[abdulasiraj]

Hey @richardjgowers I think we have to create an additional Refpoint class or modify the Point class because currently, the point class needs its own cutoff while we already provided cutoff for sphzone. let me know what you think. thanks!