I think the point is that there is a role for a bond type that looks
like a single, thick, dotted line, not solid+dotted as in aromatic; not
thin and dotted like typical "hbonds".
The fact that there is a file type that registers this suggests that it
is warranted.
Hens, for the life of me I can't find support for "partial01" in the
history of CML file readers. That was in there? Miguel will have to look
into this when he gets back. In the mean time, you can certainly use
connect. Are these animations? Connect can do a nice job of displaying
such bonds.
For example, here would be a trick to assign all "long" bonds between
specific atoms as normal-width dashed bonds, assuming there were several
frames with animation:
connect 1.6 3.0 (atomno=1) (atomno=2) create single
connect 1.6 3.0 (atomno=1) (atomno=2) modify hbond
The first creates a standard-diameter single bond. The second turns into
a dashed line. This, I think, might be even better than the partial01
bond idea, because you would have full flexibility over what is going to
be indicated and what isn't, and you could decide exactly what distances
would be displayed as dashed lines. What isn't possible at this time
(but we have discussed it as a possibility) would be something like:
connect 1.6 3.0 (atomno=1) (atomno=2) create hbond RADIUS 0.05
(SOMETHING like that, anyway), where the bond radius would be created at
the time of connection. Would you have use for that?
Bob
Angel Herraez wrote:
On 6 Apr 2006 at 15:01, Bob Hanson wrote:
I'll let others answer that. The more long-term solution would be to
drop the hydrogen bond idea -- they aren't hydrogen bonds -- and to
implement a "partial bond" idea. That's fairly complex. Please enter
it as a feature request if you like the idea.
Couldn't these partial order bonds have some relation to aromatic bonds? or delocalized
bonds, e.g. in carboxilate -COO(-) ?
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