Tailor : Descriptions

Tailor (https://github.com/gilleain/tailor) is a project that grew out of my attempts to search for ~~catmats~~ niches with Prof. Milner-White. The goal of the project was to allow users to define protein structural patterns (called 'descriptions') along with a set of associated measures. More on measures later, but first what is a description?

Here is a very simple example:

The lines don't have arrowheads, but this is implicitly a tree/DAG rather than a graph. There is a root ProteinDescription and the leaves are AtomDescriptions - the DistanceCondition is referencing the two atoms. Basically, this just defines a pattern of two amino acids (GLY, ALA) with a distance of less than 3Å between the N and O atoms.

There are still a lot of details to be worked out here. Can the groups be separated along the chain? If they can, should that require the description to be explicit as to the relationship between sibling nodes? How do we define any number of matches (as with a helix, or strand)?

After some messing about with some ideas from regular expressions, I've abandoned for now the idea of having metacharacters like ".*" or ".+" as it would be hellishly difficult to match. Consider this description:

If you wanted to have the middle two groups repeated any number of times - the equivalent of "A.*G" as a sequence regular expression - how would that work? You would have to test the torsion condition for any number of repeated groups, but that requires the 'capping' residues to be present.

In any case, the code is slowly being revived - with better tests! - and hopefully should be more usable in the New Year...

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Adamantane, Diamantane, Twistane

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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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