Dear Navid, RDKit rejects tetravalent Nitrogen by default. This thread below may help. It shows how to load the SMILES with sanitization off, then perform a partial sanitization.
https://sourceforge.net/p/rdkit/mailman/message/32589379/ Vin From: Navid Shervani-Tabar <nshe...@gmail.com> Sent: Tuesday, September 24, 2019 6:55 PM To: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Subject: [Rdkit-discuss] Problems with SMILES using MolFromSmiles Hello, I have noticed that RDKit have some problems with some SMILES when trying to use MolFromSmiles. With further attention, I have noticed that all of these SMILES include nitrogen atoms. Some examples include: [NH3]CCC(=O)[O] NC(=[NH2])C(=O)[O] NC(=[NH2])[CH2].C(=O)=O CNC(=[NH2])C(=O)[O] CNC(=[NH2])C(=O)[O] C[C@@H](C[NH3])C(=O)[O] I was wondering if there is a way to fix this issue and study those molecules. Thanks! Best, Navid
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