Thursday, 13 February 2014

Animated Algorithm: Canonical Tautomer Assignment

Effectively understanding an algorithm with only a description is difficult. Reading source code, possibly more so. Although these approaches explain the finer details, invariants and proofs, a higher level view offers clarity. A great example of this is seen at McKay's and Piperno's canonical labelling site, The Search Tree.

Tautomers are constitutional isomers of organic compounds that rapidly interconvert (Wikipedia). The most common form, is the relocation of a proton. Many computer representations are tautomer specific and distinguish different tautomeric forms of a compound. They would for example not have the same unique SMILES.

There are several approaches and algorithms for handling tautomers (Warr W, 2010). At the Daylight EuroMUG99, Roger Sayle and Jack Delany presented an algorithm for enumerating and assigning a unique tautomer (Sayle R and Delany J, 1999). From slide 20 in that presentation, there is a very nice step wise example on guanine.

This afternoon I had fun creating a animation for algorithm using an implementation I wrote last year. I've used a more complicated example that emphasises the backtracking when an incorrect assignment is made.

Being a large compound, I didn't include the keto-enol types. Also I had to modify the order (normally the nitrogens would be assigned first) to allow it be watchable in reasonable time. Each proton is placed and the hetroatoms become either a donor (green) or acceptor (blue). At several points it attempts to place two protons in each of the five membered rings. After updating adjacent atoms the mistake is identified and the assignment backtracks setting one as an proton acceptor.

Be sure to set the HD option.


Warr W (2010) shows an example labelled as "hidden tautomers". This compound presents an interesting challenge and a nice demonstration. In total there are 68 tautomers generated.



References


Warr WA. Tautomerism in chemical information management systems. J Comput Aided Mol Des. 24(6-7):497-520. 2010
Also presented at the ChemAxon 2010 UGM - http://www.youtube.com/watch?v=1C-RTD4DAJ8

Sayle RA and Delany JJ. Canonicalization and enumeration of tauomers. Presented at EuroMUG99, Cambridge, UK, 28-29 Oct 1999