A carboxylate has to be represented as C(=O)[O-]. Use ...[OH] for an uncharged carboxyl. Similarly, a tetravalent aliphatic N has to be given a + charge.
-P. On Tue, Sep 24, 2019 at 9:15 PM Scalfani, Vincent <vfscalf...@ua.edu> wrote: > 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 > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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