Jakub Adamczyk
Jakub Adamczyk
@bp-kelley Dundee comes from https://github.com/PatWalters/rd_filters. Making a note is definitely a good idea. Maybe also mark one as deprecated alias?
You're right, I found it here: https://chembl.blogspot.com/2015/02/chembl-20-released.html. They call it Dundee, not Brenk, so this is probably a better default name after all.
Still relevant. If there is a consensus that Brenk is left and Dundee can be removed, I can try making a PR for this.
I agree with keeping just one, preferably Brenk, to avoid breaking changes in [scikit-fingerprints](https://github.com/scikit-fingerprints/scikit-fingerprints), it would probably also affect [medchem](https://github.com/datamol-io/medchem). So pointing Dundee to Brenk sounds like the best option...
@mxqmxqmxq I actually requested the same thing in my issue https://github.com/snap-stanford/ogb/issues/485. I think that this is related to many definitions of scaffold split: https://github.com/rdkit/rdkit/discussions/6844. Namely, there are a few variants:...
@mxqmxqmxq I ran simple pipeline with ECFP4 (binary, 2048 bits) + RF (default sklearn settings) with different variants of the split, modifying the scikit-fingerprints code locally a bit: ``` OGB...
See https://github.com/rdkit/rdkit/discussions/6844, function `MurckoScaffold.MakeScaffoldGeneric`
@cgh2797 can this be closed now?
Now this makes sense. Raymond & Willett paper is equivalent, but docs definitely should be more precise, particularly in case of Sokal similarity. As far as I can tell, no...
Bump, still relevant