OpenEye PAINS Mapping Python Script

OpenEye advertises an additional 170 PAINS rules (versus the original 480) to accomodate data loss when converting the substructure patterns from SLN to SMARTS format. However, it was found that many of these additional rules mapped to rules that had been blocked out by Baell as part of an expanded set. These rules have not necessarily been validated as PAINS substructures.

The naming pattern for the OpenEye PAINS classification is: \"pains_{PAINS class}_{PAINS registration ID}\". If the rule has come from the expanded set, the rule is annotated as class \"pre\", otherwise it is designated with the traditional A, B, or C. 

This script was written based on the openly accessible OpenEye template scripts. 

This protocol is being made available in conjunction with an upcoming publication.