Dear colleagues,
I have encountered an instance where MolToSmiles(MolFromSmiles()) resulted
in a change of stereochemistry of a double bond. An attached figure
illustrates this.
The problematic input smiles is "C1Nc2ccc(C)cc2/C1=C1/Nc2ccccc2/C1=N\OCCOF".
The original smiles was even longer. I am afraid that this is already the
shortest version I manage to get. When I cut the methyl group
("C1Nc2ccccc2/C1=C1/Nc2ccccc2/C1=N\OCCOF"), or just shorten the long tail
("C1Nc2ccc(C)cc2/C1=C1/Nc2ccccc2/C1=N\OC"), things would go well, as shown
in the other two figures.
It does not seem to be related to the reusing of the ring closure digit
markers. The problem persisted when I avoid reusing the digits.
"C1Nc2ccc(C)cc2/C1=C3/Nc4ccccc4/C3=N\OCCOF"
Thank you for your attention. Hope you have had a good weekend by the time
you see this.
Ling
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