Combinations and Filters

So there is now the beginning of a possible re-write of the DBST that uses basically the same approach, but is a bit more flexible. The code is here, but it's still a bit rough.

The original idea seems to have been to encode arrangements of double bonds for different ring sizes as a kind of 'library'. For each ring, a particular arrangement is picked until all possible combinations are generated. As a concrete example, see this example for a napthalene skeleton:

Here, the arrangements (1, 2) are applied to each ring (A, B) and then these are combined. Of the four combinations (A1B1, A2B1, A1B2, A2B2) only three are valid. The A1B2 combination has two atoms highlighted in red that have two double bonds and one single bond.

So one way to filter the combinations is to try and type the atoms, and reject any structure that has untypeable atoms. Another possible filter rejects structures that don't have atoms that are SP2 hybridized. Both of these are from the original code, but implemented as instances of a ChemicalFilter interface.

This is quite similar - uncoincidentally- to the approach in SMSD where graph-theoretical tools are used to generate possible subgraph matches, and then a chemical filter is used to rank the results. Ranking and filtering are not quite the same, so perhaps there should be a ChemicalRanker interface? It would be a little like an Enumeration, except that it might not be a total ordering, but a partial order.

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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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