partialsmiles
partialsmiles copied to clipboard
baoilleach
SS-1: Acceptance Criteria for Diamond
Hello,
I was testing my dataset against different validation platforms and it seems like C&1&1&1 is throwing a rejection. I added it to my list because it's defined in the openSMILES as diamond, Page 21.
http://opensmiles.org/opensmiles.pdf
I'm wondering if this should be accepted by the partialSMILES? `
That's a new one on me. Most people would say that SMILES does not support extended structures. I'd love to know any program that reads that as diamond. However, as a general point, it may be that I do not support the "&", so I'll leave this open until I've checked.
Just checked the opensmiles.pdf you point to. This is in the "Proposed extensions" section, and so not part of Daylight SMILES.
Ah huh, in the proposed section it looks like the reason why it wasn't implemented was because of the & symbol conflicting with R-Groups.
RDKit can process strings like C1=CC=CC=C1(~[*:1]) so it could be better than the ampersand where the ~ is the virtual bond and the * is the virtual particle. The class can be replaced with a corresponding R-Group and we reserve & for materials like they proposed?
What are your thoughts?