Implementing the CACTVS/PubChem substructure keys

Here's the place to leave comments about my rather lengthy article on the problems I ran into while implementing the PubChem/CACTVS substructure keys, with background, pointers to the MACCS definitions, and other chunky nuggets of feature key wisdom.

subgraph enumeration

I've started a series on subgraph enumeration. In Part 1 I present a brute force enumeration algorithm, modify it to remove duplicates, and post-process the results to generate canonical SMARTS for each subgraph. In Part 2 I develop a new algorithm which is about 3.5 times faster.