[Cdk-user] Smiles parser and explicit aromaticity

I have a question regarding the CDK SmilesParser and aromaticity. Example below: input is a Smiles structure with 3 aromatic rings, 15 aromatic bonds in total. The CDK parses into an atom container with only 11 aromatic bonds. I was wondering: if the structure has explicit aromaticity bonds,

Re: [Cdk-user] Smiles parser and explicit aromaticity

Hi Mark, On Thu, Aug 12, 2010 at 6:07 PM, Mark Rijnbeek ma...@ebi.ac.uk wrote: I was wondering: if the structure has explicit aromaticity bonds, would it not be better to preserve this in the container? Rather than overruling it with the CDK's aromaticity detection. AFAIK the SMILES

Re: [Cdk-user] Smiles parser and explicit aromaticity

All, On Thu, Aug 12, 2010 at 6:43 PM, Egon Willighagen egon.willigha...@gmail.com wrote: AFAIK the SMILES specification dictates that the parser detects the aromaticity... For example... the parser needs to decide if something is aromatic or anti-aromatic... both are validly encoded with