Bob, I think it would be a good idea for you to coordinate with others on
the list to determine what the commands should be.
I'd like to do that. Let's bat around a few possibilities. I know my own
proposition is a moving target. The issue for me came up as I was
rewriting the documentation. I have about 30 minutes here, then I'm gone
for the day. I think most interested parties are online today. How about
if we say:
Present some options today/tomorrow.
I might try out something on the weekend, just to get my feet wet.
Early next week narrow it down to one option for Miguel or me to implement.
I would like to start fresh -- ignore my previous suggestions -- and
propose:
OPTION BH.1:
set connectmode <bond type>
select (atom expression)
connect <min distance> <max distance> (target atom expression)
where <bond type> includes SINGLE, DOUBLE, TRIPLE, AROMATIC, HBOND, NONE
and parameters to connect are optional (a single number being <max
distance>)
and no further changes to wireframe
examples:
select (carbon)
set connectmode DOUBLE
connect 1.3 1.5 (oxygen)
set connectmode SINGLE
connect 1.5 1.7 (oxygen)
set connectmode NONE
connect 1.7 1.9 (oxygen)
Now, the question becomes:
What should be the behavior of connect if bonds are already present.
Should those be ignored or replaced?
Currently, connect is set to ignore bonds that are already present, in
an odd sort of compementarity to how wireframe ignores bonds that are
not already present.
Option BH.1 proposes that connect would do exactly what it says --
connecting with a certain type of bond -- regardless of what is there
already.
Rationale: You can be as specific as you want in selecting the atom set
and now the distance range, so that suggests to me that there should be
no surprises. The command does just what it says and not
"connect-unless-not-already-connected"
Bob
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