Re: [Cdk-user] canonical chiral smiles with free electron pair

Hi John, Thank you very much for your fast and very helpful response. Just to be sure: I have to imagine the electron pair between the "@" and the "]", right? So it is always the first "substituent" after the central atom. Thank you for the link and the comment to our code! Best regards, Lina

Re: [Cdk-user] canonical chiral smiles with free electron pair

> > I have to imagine the electron pair between the "@" and the "]", right? Yep that's correct. It's technically an extension but is widely supported at least by CDK, Open Babel, ChemAxon, ChemDraw, OpenEye, CACTVS. It looks RDKit doesn't support it, not Indigo (at least in the version I have

Re: [Cdk-user] canonical chiral smiles with free electron pair

Hmm, actually from that screenshot it looks like Indigo supports @@ but not @... CCC[S@](C)=O CCC[S@@](C)=O Regards, John W May john.wilkinson...@gmail.com On 26 November 2015 at 18:14, John M wrote: > I have to imagine the electron pair between the "@" and the

[Cdk-user] canonical chiral smiles with free electron pair

Hi all, we used the attached java code utilizing CDK 1.5. to create a canonical chiral smiles from the input which was the attached Esomeprazol.sdf. The result is: Cc1cnc(C[S@@](=O)c2[nH]c3ccc(cc3n2)OC)c(C)c1OC To determine an explicit chirality from the smiles you need the four different

Re: [Cdk-user] canonical chiral smiles with free electron pair

Hi, I'm not entirely sure what the question was but - The lone-pair is treated like an implicit hydrogen and is placed where the central atom is. In the internal representation this means one of the neighbours will also be the central atom. For example in (your email client might cut the tail