Tests that Pass, Tests that Fail

The AMG (alternative molecule generator) is now good enough to run proper tests on, with help from Tobias Kind who has long promised - or threatened, perhaps :) - to test a structure generators. It should lead to software that is of more than theoretical interest.

Currently, there is a download available from github, or it can be built from the project directory if you are familiar with ant and are willing to change the build.properties file to point to a CDK directory. There is an instructions.txt file, with some examples of usages; the -h flag also works as might be expected.

As for passing tests, it currently does better with hydrocarbons - CnH2n + x for x in {-2, 0, 2}. However, it's starting to improve on the more mixed formulae, with oxygen, nitrogen, and so on. The two child-listing methods (filter/symmetric) have different behaviour, annoyingly.

Looking at one of the two pairs of duplicates in the set of C6H4 structures shows why it fails. The method here is the symmetry one, where only the minimal representative of an augmentation under the automorphism group of the parent is chosen. Sadly, this picture shows a case where the method fails:

The parent is highlighted in grey, and the child graphs (A, B) are shown on left and right. The central image shows how both 5a and 5b are adding different sets of bonds. Since the automorphism group of the parent has only the identity permutation (ie: it is trivial) any set of bonds will be equivalent.

I had realised that this could happen, but I foolishly assumed that it was rarer than this. That may be the case for simple graphs, but apparently not for multigraphs like this...

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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

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