On Oct 20 2004, Bob Hanson wrote:
We use exactly this approach in CML (in fact the use is an "order" attribute on bond. We deliberately do not use numbers so that people are not tempted to overinpterpret "1.5". We use "S" or "1" for single, "A" for aromatic, etc. What these mean are deliberately undefined.
Miguel wrote:
> > So, what do people think about this ...
> > We introduce a new scripting command called 'bondOrder'.
> > bondOrder [ 1 | 2 | 3 | aromatic | hbond ]
> > It applies to all pre-existing bonds within the current set of selected
> atoms ... just like 'wireframe'
> > It respects the 'set bondmode [ and | or ] ' setting ... just like
> 'wireframe'
>
a. Need the possibility of bond order of 4. b. What are you thinking "aromatic" will mean? c. If you mean "partial" for "aromatic," you might consider the possibility of 0.5, 1.5, 2.5, 3.5, where these show with one of the lines dotted.
> Q: Is there a word other than 'bondOrder' that we should use?
>
In Jmol I suspect the main reason is to create additional bonds with attributes mainly for display. I would counsel against doing serious computation with bond orders. If you do, then it would be useful if Jmol and CML could be compatible. Note that representing a double bond by two single bonds use to be quite common but I think the only place that uses it now is PDB (and possibly CSSR if that still exists). Suggest you maintain compatibility but don't promote it.
P.
sounds right to me.
Bob Hanson
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