The other issue is distinguishing hbonds as calculated and as file-determined.
We should be able to selectively display/undisplay these. Something associated
with the hbond mask should do the trick here.
Miguel wrote:
When we set the size on an hbond, the hbond calculation code is being run
because it has never run before.
This is fine. Just don't run the calculation if setting the size = 0. If setting
the size positive, it's pretty clear that one is asking for the calculation. It
seems to me no big deal. (But see below)
Once the hbond calculation code has been run, it will never run again ...
even if we do a 'connect delete hbond ...' because the hbond code does not
currently know that hbonds can be deleted.
Obviously we need
hbonds calculate
which might have two flavors -- Rasmol and Jmol, for example.
My thoughts:
* we need to separate hbond size control from hbond autocalculation
I don't see any great need for this. The two are already separated; we need that
default action. Something else must be wrong here.
* doing so will break compatibility with existing scripts that use 'hbond
on' run the hbond autocalc code
do not break current compatibility, please.
* it doesn't seem to me that this will be much of a problem for many
people ... but I don't really know
see above.
* it seems to me that this should be something like 'hbond calculate' ...
or something similar.
That's what is needed
* this would be distinct from 'hbond on/off/<size>' ... which would only
affect the display of current hbonds
and default to calculate. We could have
hbond file on/off/size
that only sets the on/off/size for file-based hbonds
hbond calc on/off/size
that only sets the on/off/size for calculated hbonds, with autocalculation
hbond on/off/size
that defaults to both, with autocalculation -- the status quo
Thus:
hbonds on
#status quo
hbonds file off
hbonds calc on
#recalculate hbonds and only show calculated (undoes a delete hbonds)
hbonds on
hbonds file off
#don't recalculate; show only already-calculated hbonds
hbonds file on
hbonds calc off
#just show file-based hbonds
load <model>
hbonds file on
#re-install deleted file-based hbonds
If you are worried about actually deleting file-based bonds, this is not an
issue of hbonds. We are doing it on all bond types. That's what connect is for
-- to modify the file-based or calculated bond information.
Q: What EXACTLY is causing restrict to turn on the hbonds?
Bob
--
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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