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Showing posts from December, 2016

Tailor : Descriptions

Tailor (https://github.com/gilleain/tailor) is a project that grew out of my attempts to search for catmatsniches 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 st…