Skip to main content

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 :)

Comments

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.
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.
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.
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...
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.

Popular posts from this blog

How many isomers of C4H11N are there?

One of the most popular queries that lands people at this blog is about the isomers of C4H11N - which I suspect may be some kind of organic chemistry question on student homework. In any case, this post will describe how to find all members of a small space like this by hand rather than using software.

Firstly, lets connect all the hydrogens to the heavy atoms (C and N, in this case). For example:


Now eleven hydrogens can be distributed among these five heavy atoms in various ways. In fact this is the problem of partitioning a number into a list of other numbers which I've talked about before. These partitions and (possible) fragment lists are shown here:


One thing to notice is that all partitions have to have 5 parts - even if one of those parts is 0. That's not strictly a partition anymore, but never mind. The other important point is that some of the partitions lead to multiple fragment lists - [3, 3, 2, 2, 1] could have a CH+NH2 or an NH+CH2.

The final step is to connect u…

Generating Dungeons With BSP Trees or Sliceable Rectangles

So, I admit that the original reason for looking at sliceable rectangles was because of this gaming stackoverflow question about generating dungeon maps. The approach described there uses something called a binary split partition tree (BSP Tree) that's usually used in the context of 3D - notably in the rendering engine of the game Doom. Here is a BSP tree, as an example:



In the image, we have a sliced rectangle on the left, with the final rectangles labelled with letters (A-E) and the slices with numbers (1-4). The corresponding tree is on the right, with the slices as internal nodes labelled with 'h' for horizontal and 'v' for vertical. Naturally, only the leaves correspond to rectangles, and each internal node has two children - it's a binary tree.

So what is the connection between such trees and the sliceable dual graphs? Well, the rectangles are related in exactly the expected way:


Here, the same BSP tree is on the left (without some labels), and the slicea…

Listing Degree Restricted Trees

Although stack overflow is generally just an endless source of questions on the lines of "HALP plz give CODES!? ... NOT homeWORK!! - don't close :(" occasionally you get more interesting ones. For example this one that asks about degree-restricted trees. Also there's some stuff about vertex labelling, but I think I've slightly missed something there.

In any case, lets look at the simpler problem : listing non-isomorphic trees with max degree 3. It's a nice small example of a general approach that I've been thinking about. The idea is to:
Given N vertices, partition 2(N - 1) into N parts of at most 3 -> D = {d0, d1, ... }For each d_i in D, connect the degrees in all possible ways that make trees.Filter out duplicates within each set generated by some d_i. Hmm. Sure would be nice to have maths formatting on blogger....

Anyway, look at this example for partitioning 12 into 7 parts:

At the top are the partitions, in the middle the trees (colored by degree) …