### Visualising Ring Equivalence Classes in Jmol

As promised (in the previous post) I've now made Jmol scripts to show the atom/ring equivalence classes. I still think that the ring ones are more clear, but I suppose it depends on what aspect of the symmetry of the structure is needed. As an example:

Shown here is a C70 structure, with coloured circular plates at the centre of each face. It should be clear that there is an axis of symmetry running through the middle, from one blue plate to the other. Around the blue is a ring of green, and 5 rings in between.

The slight difficulty in all this was working out the ring equivalence classes. There is an existing CDK method to do this - in the SSSR ring finder - but it seems to give too many classes. The way I did it was to first find atom equivalence classes (or 'orbits') using signatures. Then each ring is a circular list of the orbit indices : which I'm going to call a 'ring code'. See this image for illustration:

These two rings (A and B) have the same ring code, written as the smallest concatenated string formed from their orbit indices. In other words, the signatures of each atom in the ring is converted to a number based on that signatures index in a list of all the signatures for all the atoms. Obviously other atom-equivalence class methods could be used to find the initial orbits; the rest of the procedure would be the same.

I do wonder if it would be quicker to just find the orbits of the dual of the embedding. However, that involves making that embedding first, so probably not...

Sharing some common points with chiral compound. Chiral synthesis study may benefit from the post.

### 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) …

### Common Vertex Matrices of Graphs

There is an interesting set of papers out this year by Milan Randic et al (sorry about the accents - blogger seems to have a problem with accented 'c'...). I've looked at his work before here.

[1] Common vertex matrix: A novel characterization of molecular graphs by counting
[2] On the centrality of vertices of molecular graphs

and one still in publication to do with fullerenes. The central idea here (ho ho) is a graph descriptor a bit like path lengths called 'centrality'. Briefly, it is the count of neighbourhood intersections between pairs of vertices. Roughly this is illustrated here:

For the selected pair of vertices, the common vertices are those at the same distance from each - one at a distance of two and one at a distance of three. The matrix element for this pair will be the sum - 2 - and this is repeated for all pairs in the graph. Naturally, this is symmetric:

At the right of the matrix is the row sum (∑) which can be ordered to provide a graph invarian…