-
Notifications
You must be signed in to change notification settings - Fork 227
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
SMILES output wrong for strange CO species. #183
Comments
I think the problem is a missing check in fromAdjacencyList() that rejects wrong or incomplete adjacency lists like the one you mentioned:
Where did you find it? |
We made it up as a test. |
I think that is what is happening. fromAdjacencyList() is reading that adjacency list assuming all hydrogen atoms are explicitly present as saturateH=False is standard for that function. Can you print the charge attribute of the two atoms? Also can you try it with fromAdjacencyList(saturateH=True)? |
This is a deprecated issue. The adjlist should have explicit hydrogens or if it is carbon monoxide it should be a triple bonded adjlist with 1 lone pair on both carbon and oxygen. |
I'm not sure what this represents (still not used to the lone pairs column) but I'm pretty sure there are only two atoms, a C and an O
However, the SMILES (generated via RDKit) is
[CH2]O
Strangely, RDKit agrees that there are two atoms:
so I'm not sure what's going on. Perhaps start with some more unit tests on SMILES output from strange things?
The text was updated successfully, but these errors were encountered: