Jan wrote:
side effect of connect should be to
set bondmode AND
and select the newly (dis)connected atoms
or which may be better, define a set
define CONNECT <AND-atoms>
oooh, I REALLY dislike "side effects" doing hidden settings changes.
Note that the effect of the connect is not the same as set bondmode AND.
That is, there is no current way to target those bonds except with
another CONNECT command. You have targeted very specific bonds, yet
there is no select for bonds, only atoms. The "selection" cannot be
reproduced in prior methods, because the way connect operates, it does a
sequence of two-atom-specific bond settings based on distance, not
AND/OR sets.
define double1 CONNECT
this is what is impossble (currently).
connect 1.3 2.0 HBOND NEW (hydrogen) (oxygen)
select hydrogen and within(2.0, oxygen) and not within(1.3, oxygen)
or oxygen and within(2.0, hydrogen) and not within(1.3, hydrogen)
hbond 2
^ this may *not* be the same as the following
to
connect 1.3 2.0 HBOND NEW 2 (hydrogen) (oxygen)
I agree.
I vote for:
define CONNECT <AND-atoms>
and a distinct radius of hbonds 1 (dotted line) by default.
So, for example, say you were setting the short C-O bonds to be double
bonds and you had
(O=C)-(C=O)
So you use:
connect 1.2 1.3 DOUBLE (carbon) (oxygen)
Now you select "AND" and you have selected in addition the C-C bond for
whatever happens next, because all you have done is select the four atoms.
My point is that an operation on bonds cannot be reproduced as an
operation on atoms. They are fundamentally two different classes, but
code-wise and figuratively speaking.
Unless we invent a new selection mechanism that targets bonds, it can't
be done. (OK, we could do that, but it would be a completely new idea,
invented just so that we aren't mixing in an extra radius integer in the
CONNECT command. Do we want to make this that complicated? Maybe...)
Perhaps this is the time to go beyond "set bondmode AND/OR" which to me
has always seemed a very odd and primitive way to target bonds.
I'm curious about this rendering/connecting dichotomy. Didn't Miguel
originally implement this along the lines of wireframe, arguing that it
WAS a rendering issue? "Connections" in Jmol are just "class Bond",
which is specifically a viewer rendering class. To me, I see the whole
"connect" issue as a subdivision of rendering -- all we are really doing
is creating a new rendering cylinder object, which has five specific
properties: atom1, atom2, order, radius, and color/translucency.
That said, I like the idea of selecting BONDS as opposed to ATOMS so
that these items could all be changed selectively. But that's a whole
additional concept.
Maybe what we are talking about is something like
selectBonds 1.2 1.4 [|EXISTS|NEW] (carbon) (oxygen)
connect SELECTEDBONDS DOUBLE
color SELECTEDBONDS red translucent
wireframe SELECTEDBONDS 0.2
Maybe?
Bob
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