Dash logoUC San Francisco logo

OpenEye PAINS Mapping Python Script


Davies, Julia (2019), OpenEye PAINS Mapping Python Script, v2, UC San Francisco Dash, Dataset, https://doi.org/10.7272/Q6Q81B8F


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.


Please refer to Materials and Methods and Supplementary Material of the associated manuscript, Small molecule inhibitors of the human recombination-associated ATPase, RAD54

Usage Notes

Requires acces to a server with Python 3 and OpenEye installed. 

To run the script:

./oepains_table.py file.sdf > out.txt