Thread by @baoilleach

#11thICCS Robert Schmidt on Comparison and Analysis of Molecular Patterns on the Example of SMARTS

Gives example: [O,N]-!@c(:c):[a!c] and visualization via Smarts Viewer. Red indicates negation - matches everything except whatever.

The molecular pattern comparison problem. Difficult to compare patterns. Are two patterns the same? One may match a subset of the others.

Motivation: why interesting? Lots of SMARTS patterns filters. Any difference between Dundee filters and BMS filters? How similar is one set of filters to another?

How do we compare two SMARTS nodes? Extended valence states JCIM 2014, 54, 3, 756. Annotate each node with property values. 20071 atom type states that can be annotated with SMARTS. Set bits to true for all feasible states.

For edges, we only need 9 bits to cover all possibilities. Distinguish between cyclic and non-cyclic ones.

What's the relationship between CCN and CCC[N,O]. Create the fps for the nodes and edges. Match via a clique-based approach to get correspondances. (ed: a faster approach would be to use the same approach as used for SMARTS matching)

Node similarity is based on statistical analysis of node occurences.

Is pattern A more specific than pattern B? Equivalent is whether each node of A more specific than B?

SMARTScompare can also handle recursive SMARTS via recursive calls. (ed: impressive!)

Gives examples taken from BMS set and Inpharmatica set. Is there any pattern than is more generic or more specific?

Took 400 patterns with ~1000 matches within 370M molecules from ZINC. How similar are pattersn from set A to set B. Compare patterns in terms of matches to molecules. (ed: missed some details - sorry)

Allows search for specific patterns, search for generic patterns, similarity assessments.

Future work will be supporting remaining SMARTS features. Improve recursive SMARTS, and developing a unique SMARTS repr.

Ed: I think this would be useful even for preparing a SMARTS to match a functional group, as you could find matches to other existing patterns and see whether it would make sense to adjust your own one.

Ed: Questioner is wondering about applicability. Doesn't get how awesome this is. It's the sort of thing we've discussed in-house from time to time.

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