Monday, August 22, 2016

Finding the reference molecule for a pKa calculation using RDKit

This is prototype code related to this project.  I use Histamine as an example which has two ionizable sites: a primary amine and an imidazole ring.

The code figures out that imidazole is the best reference for the imidazole ring, while ethylamine is the best reference for the primary amine.  The code does this by figuring out which atom is being deprotonated, computes the Morgan fingerprint around this atom, and compares it to the Morgan fingerprints of imizadole and ethylamine.

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