Add "select" option to hbonds command

[Elaine Meng]

Add "select" option analogous to that in clashes/contacts (less crucial now that "hbondatoms" selector has been added, however)

[Eric Pettersen]

Batch does in fact "do things" as is. Specifically, if batch is true then having a main atom spec that doesn't actually select any atoms will not produce an error, nor will having a 'restrict' atom spec that selects no atoms. Otherwise, those would produce/throw errors.

--Eric

[Elaine Meng]

Oh, my bad… I’d taken the “batch” description straight from Chimera documentation.  I will put it back into the ChimeraX docs with revisions as you just explained.

[Eric Pettersen]

Okay, added "select" keyword to the hbonds command. The question is, do we also put it in the tool GUI? And if so, where?

[Elaine Meng]

Clashes/Contacts has a separate section "Treatment of results" with:

Select atoms
Reveal atoms of interacting residues
Assign atomic attribute...

...so possibly you could create an analogous section in the H-bonds dialog and move the "reveal" option there so that it contains (in either order):

Select atoms
Reveal atoms of H-bonding residues

I might put it between the "Limit" and "Write" sections but I don't feel strongly.  Also depends on whether you think adding a section would make the dialog too long and hideous.

[Eric Pettersen]

Okay, added the option to the GUI as suggested.

[Elaine Meng]

Changed my mind on the GUI, if it's not a giant pain I'd say to put Reveal back where it was and put Select atoms up in that same section right under it, instead of making a new section.  Sorry.  Willing to be convinced otherwise if you have an opinion.

[Elaine Meng]

Given our discussion, ignore the previous comment  and stick with my initial suggestion as to the arrangement of the GUI.  Thanks!