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