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lone pair rendering

JCP now has minimal lone pair display. I would prefer the layout to be at the corners of a square, rather than on the edges. Videlicet, they are currently only at N, W, S, E; I think that NW, SW, SW, and NE would be better.

Strangely lone pairs don't seem to appear in CML files when written out, but Egon says he will look at this. Perhaps I should file a bug report...
Oh, and radicals are implemented too, but I don't have a picture of that (see right). They are in different generators, but I guess a single 'DotGenerator' could do both :)
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Kirill said…
According to this IUPAC Recommendations (section GR-5.2 Lone pairs):
Isolated lone pairs should be positioned, like unpaired electrons, close to the atom with which they are associated. They should normally be positioned exactly above, below, to the left, or to the right of the atom label, with the two dots of the lone pair parallel to the closest side (horizontally if above or below the label, vertically if to the left or the right). Positioning of lone pairs at other angles should be strongly avoided unless it is impossible to do otherwise.
To illustrate the latter point, there is an example of ClF3 where two lone pairs are shown to NE and SE of Cl atom.
15 February 2009 at 15:06
Kirill said…
Do they (lone pairs) actually have to be present in CML file? I think this is a matter of representation / style. The lone pair in ammonia is there irrespectively of whether we want to see it or not.
15 February 2009 at 15:10
gilleain said…
wow - I didn't know there were so many ways to get a chemical diagram wrong! :)

That looks like a very useful document, thanks.

I had assumed that the lone pair should be drawn where a bond would be. So an COH would have a trigonal planar structure...

This is true that lone pairs are implicit. I was distracted by the fact that the CDK requires there to be an explicit lone pair object attached to an atom.

I guess the situation is a lot like hydrogens, actually.
15 February 2009 at 16:01
Egon Willighagen said…
Gillean, looks great!

Kirill, the LPs are there always, sure. However, diagrams are somewhat special, where you might want to put focus on some lone pairs, not all. For example, those involved in a reaction. This is why one would be interested in serializing this to CML.

Regarding the oxygen lone pairs... it actually has two lone pairs, and the diagram chooses to show only one...
15 February 2009 at 16:58
Kirill said…
Sure, it would be great to show where lone pair is, especially if that adds clarity to the sketch. Another IUPAC Recommendations (you see, I am promoting my own work here), p. 1942, top, show two examples of trigonal pyramidal confuguration due to lone pair. If you do not draw this lone pair, you may not even realise that sulfur and phosphorus are chiral atoms there.
15 February 2009 at 18:03
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