PVR numbering scheme not solution to all woes : film at 11

On a whim, I decided to try generating all adjacency matrices with the property that they are PVR numbered. The short summary of that link is that a matrix can be expressed as a sequence of positive integers by considering each row of the matrix as a binary number.

The point of doing this (I thought) was that you can number a molecule in such a way that the adjacency matrix is PVR-numbered, and that this is canonical. So my cunning plan was to generate all sequences of n numbers that are partially ordered, choosing them from [1, 2ⁿ] to give all non-redundant (simple) graphs with n vertices.

Unfortunately, it seems like this can't work:

This image shows all adjacency matrices for n = 3 which are PVR-numbered. They are made by backtracking through all sequences of integers with a partial order, pruning the solutions using the symmetry of the matrix as a constraint.

Anyway, the point is that the first two graphs are clearly isomorphic! More simply, they both represent propane. Maybe this is well known, but it's a surprise to me...

Comments

Egon Willighagen said…

The method used by the previous deterministic structure generator used a similar approach... If just looking at rows may not be enough... what happens if you would look at the ordering of the columns too?

21 May 2009 at 15:23

Anonymous said…

What a great web log. I spend hours on the net reading blogs, about tons of various subjects. I have to first of all give praise to whoever created your theme and second of all to you for writing what i can only describe as an fabulous article. I honestly believe there is a skill to writing articles that only very few posses and honestly you got it. The combining of demonstrative and upper-class content is by all odds super rare with the astronomic amount of blogs on the cyberspace.

30 January 2011 at 19:05

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the

General Graph Layout : Putting the Parts Together

An essential tool for graph generation is surely the ability to draw graphs. There are, of course, many methods for doing so along with many implementations of them. This post describes one more (or perhaps an existing method - I haven't checked). Firstly, lets divide a graph up into two parts; a) the blocks, also known as ' biconnected components ', and b) trees connecting those blocks. This is illustrated in the following set of examples on 6 vertices: Trees are circled in green, and blocks in red; the vertices in the overlap between two circles are articulation points. Since all trees are planar, a graph need only have planar blocks to be planar overall. The layout then just needs to do a tree layout on the tree bits and some other layout on the embedding of the blocks. One slight wrinkle is shown by the last example in the image above. There are three parts - two blocks and a tree - just like the one to its left, but sharing a single articulation point. I had

Some Stuff

Search This Blog