select by minimum/maximum length selects non-pseudobonds

[Elaine Meng]

The select command minimumLength and maximumLength options were documented (and I think tested back then) to apply to only pseudobonds. However, now when I use these options, it seems like all atoms and bonds are selected too. For example:

open 1zik
hbonds reveal true showdist true
select max 3

... this does appear to select the proper subset of pseudobonds, but also the entire atomic structure. Reassign as needed.

[Elaine Meng]

I understand that technically, these options are applied as filters, so from the programmer perspective selecting everything (including non-pseudobonds) may be expected if the specification is blank.  However, I wonder if there is a way to make this more intuitive.  If a user is trying to select all H-bonds shorter than some value, they are unlikely to think of putting the pseudobond model number in the command in addition to the length cutoffs. What do you think about making the presence of either length option also limit the selection to pseudobonds only?

[Tom Goddard]

The select command with no object specifier selects everything, and the maximumLength, minimumLength options just filter out long and short pseudobonds. So "select max 3" is expected to leave all atoms selected.

Maybe you have a better way to reconcile the fact the default select behavior with no objects with these options.

minimum_length : float or None

Exclude pseudobonds shorter than the specified length.

maximum_length : float or None

Exclude pseudobonds longer than the specified length.

[Tom Goddard]

Could have presence of max/min deselect all non-pseudobonds. Would that apply even if objects are specified in the command that include atoms?

[Elaine Meng]

Yes, my suggestion was that the presence of either length option would imply selecting only pseudobonds.  If people understand that these options apply to pseudobonds (not bonds) I really don’t think they would combine them with a spec, except a particular pbond model number if there is more than one pbond model present.  I can document this and also show these pbond options in a separate usage line, if you two think that this behavior would be OK.

[Tom Goddard]

Ok. If minimumLength or maximumLength is specified with the select command then only pseudobonds are kept in the object specifier.