Re: [Rdkit-discuss] Nitrogen Valence

Hi, If the compound is neutral overall and there is a single H where you drew it, then a valid RDKit SMILES for the nitrogen-containing terminal group is C[N+](C)(C)[NH-], which is one of the forms I gave earlier. It is not a zwitterion. Rather, it represents a dative bond. (I am not sure that

Re: [Rdkit-discuss] Nitrogen Valence

Hi Peter, Thank you for your reply. I did not quite understand what you mean by 'But this makes no sense'. Also the SMILES you tested are zwitterionic form. In this link http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization, the zwitterionic form seems suitable for N=O, N#N, not for

Re: [Rdkit-discuss] Nitrogen Valence

The problematic part is just the beginning of your would-be SMILES: N=N(C)(C)C. The rest is correctly parsed. But this makes no sense. Perhaps you mean one of the substructures illustrated in the attached (which at least satisfy normal valence rules). If not, perhaps you could attach a structural

Re: [Rdkit-discuss] Nitrogen Valence

Dear Greg, Thank you very much for the suggestions. It works for me! Here is the SMILES of one molecule that I am looking at: N=N(C)(C)CC(CN1N=CN=C1)(O)C2=C(C=C(C=C2)F)F Any better alternative will be appreciated. Thanks, Yuran On Thu, May 11, 2017 at 10:49 AM, Greg Landrum

Re: [Rdkit-discuss] Nitrogen Valence

On Thu, May 11, 2017 at 4:24 PM, Yuran Wang wrote: > I have a question regarding the available valence of Nitrogen. It seems > only 3 is available in the default setting (atomic_data.cpp). Why is it > kept to only 3, and not extended to include 4 and 5? If I change it

[Rdkit-discuss] Nitrogen Valence

Hey, I have a question regarding the available valence of Nitrogen. It seems only 3 is available in the default setting (atomic_data.cpp). Why is it kept to only 3, and not extended to include 4 and 5? If I change it locally to include 4 and 5, will it cause any problems? I am aware that I could