openff-toolkit icon indicating copy to clipboard operation
openff-toolkit copied to clipboard

Add normalization code

Open lilyminium opened this issue 2 years ago • 0 comments
trafficstars

Is your feature request related to a problem? Please describe.

Add code that "normalizes" unusual SMARTS patterns. This came up recently in both Lorenzo's parameter analysis and at https://github.com/MobleyLab/FreeSolv/issues/51 . The code already exists for NAGL, so upstreaming it into the toolkit might be worthwhile.

Describe the solution you'd like

Normalization support in the toolkit.

Describe alternatives you've considered

This is a one-liner in RDKit -- rdkit.Chem.MolStandardize.rdMolStandardize.Normalize -- so it's not too much of a hassle to leave it separate. OpenEye has reaction support but I don't think has the RDKit normalization transformation catalogue easily usable.

Additional context

lilyminium avatar Dec 11 '22 03:12 lilyminium