rdkit-blog/posts/2024-01-11-using-abbreviations

Question

rdkit-blog/posts/2024-01-11-using-abbreviations

Opened this issue 9 months ago · 2 comments

RDKit blog - Using abbreviations in the RDKit

Making more compact structure drawings.

https://greglandrum.github.io/rdkit-blog/posts/2024-01-11-using-abbreviations.html

Answer 1 · 2024-01-15T09:24:31.000Z

Just a note that the 5th image has the CO2H abbreviation 'the wrong way around' but it's correct in other earlier depictions. Maybe something to look into.

Answer 2 · 2024-01-15T11:33:01.000Z

Just a note that the 5th image has the CO2H abbreviation 'the wrong way around' but it's correct in other earlier depictions. Maybe something to look into.

Nice catch. The abbreviations code sets an additional property on the atoms which is used when molecules are drawn with the bond coming from the right. This information is not present in the CXSMILES, so the drawing afterwards can't use it.

I think that's going to be non-trivial to address, but at the very least I can update the text in the blog post to make it clear that things aren't actually being "round tripped".