Hello, I have seemed to hit a wall with what seems like a simple task.
First, I have ~9800 compounds that have a primary amine for a reaction that I am completing in rdkit. About 250 of those compounds have a tertiary alkylamine that is most likely protonated at pH 7.4. The dataset is a set of smiles strings for which the tertiary amine is not protonated. I thought this would be easy enough to fix, just use a smarts substructure search, set the formal charge on any hits to one and then AddHs, sanitize, embed, and then minimize. Well, what I get is [N+] with all the other carbons with explicit atoms in the resulting smiles files, and if output to sdf I get a positively charged diradical positioned at the tertiary nitrogen. Reading through the cookbook and this mailing list gave me no other preferred methods to protonate nitrogen. There were some deprotonation examples. Do I have to add the atom and create the bond manually? If I have missed something then please point me to a link that I overlooked. Thank you for such a great tool Brian Bennion
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