feature or issue?

[egonw]

@johnmay, I really do not know if this is a bug or a feature, but I just notice this. Given the following two SMILES, depiction in CDK Depict doesn't work for the second:

[C@@H]1(OC([C@H](O)[C@H]([C@@H]1O)O)O*)CO
[C@@H]1(O[C@H]([C@H](O)[C@H]([C@@H]1O)O)O*)CO

I am attempting to define the stereo of the last stereocenter, just as a visual check, so that I can attach it as R group to various T2 toxins, see https://social.edu.nl/@egonw/112302962828702865

[johnmay]

I presume it works if you don’t annotate the CIP labels.

CIP rules do not say anything about undefined atoms. The code tries to label as much as it can leave centres which may be R or S as unlabelled.

Note this does not mean they are undefined but a global label has no meaning. I’ll take a look as it should not throw and exception

[egonw]

CIP rules do not say anything about undefined atoms. The code tries to label as much as it can leave centres which may be R or S as unlabelled.

Ah, I did not mean about the CIP (something we did indeed discuss before), but should it throw an exception?

[johnmay]

It's the CIP throwing the exception.

[johnmay]

I need to find time to look at it, probably a simple fix.

[egonw]

I need to find time to look at it

not urgent