kyleabeauchamp/gaff2xml — pull request #3 by jchodera (2013-10-26 16:38:36+00:00)
Title: Added test for all drugs database (Zdd) from ZINC.  Test currently reveals some possible issues.

This test uses the OEChem OpenEye tools to iterate through the ZINC all drugs database (Zdd), using system_checker to compare forces between LEaP- and gaff2xml-parameterized versions of the molecules.

The test currently fails on the first molecule with a potential atom ordering or charge ordering issue.

Note that OEChem is currently only used to slice up the multi-molecule mol2 file here into individual mol2 files, but I plan to make the test more elaborate by using Omega to generate multiple conformations in future versions.