Greg Landrum

I think, again, that I don't understand the question. You can define substructure queries using any of the molecule input formats the RDKit supports. SMARTS is probably the most expressive...

@ShangChien please share an example (a CXSMILES is fine) of a type of molecule you would like to be able to enumerate. Maybe it's possible already.

@hollisullivan27, I don't understand your question; both examples in the blog post have a fragment which has multiple attachment points. Can you be specific, ideally including molecules, what you want...

Hi @xescape. This is exactly why the section of the blog post which says: "Remove any R groups which have more than one dummy atom. This happens if an R...

Hi @cthoyt, sorry I'm so slow to reply to this one; I missed the notification and am just now seeing it. I'd be happy to mention using the chembl_downloader here...

@DocMinus yes, this approach should work for those types of transformations as well. You just need to write a reaction SMARTS which performs the modification you want.

@sunhwan : no, the constraints can only be applied as distances. To get better ring conformers, I would suggest trying out the `srETKDGv3` parameters (described here: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00025). You do that...

@sunhwan: you really should AddHs() before generating conformers; that should dramatically improve the quality of the comforters you get.

@chem555: They are not. That's a step you need to do yourself if you think it's important. The conformers which come from ETKDG tend to be pretty good, so you...

@ssrb19 in order for me to be able to help here you need to share the molecule and constraints that you used