Open Babel conformer search

Now that we have the new xtb plugin and its support for CREST conformer searches, do you still view an Open Babel conformer search as crucial for a 2.0 release? It is listed as such in the roadmap.

If so I could look at writing a Python script for one, if that would be helpful.

Yes, absolutely. Conformer searches with Open Babel and RDKit take a few seconds vs. minutes to hours with CREST.

Moreover, a collaborator showed that CREST (and ML methods trained on those geometries) don’t predict bioactive conformations well because they can’t account for interactions with the protein / environment. So diverse geometries from RDKit (or Open Babel) are better suited:

“Conformer Generation for Structure-Based Drug Design: How Many and How Good?”
doi: 10.1021/acs.jcim.3c01245

Which is a long way of saying “yes, the Open Babel search dialog is coming soon”

On the other hand, CREST scripts for protonation / microsolvation, etc. would be great.

Ok, so you’re handling the Open Babel implementation yourself and my offer to write a script is not needed? :slight_smile:

I have a branch (among many) on my laptop … hopefully should be up today.

Thanks though!

Work in progress: Add conformer search box by ghutchis · Pull Request #1507 · OpenChemistry/avogadrolibs · GitHub

Seems like it might take a patch on the Open Babel side to grab all the conformers to CJSON.