On Tue, May 26, 2009 at 6:12 PM, Noel O'Boyle <[email protected]> wrote: > Either is valid for benzene according to OpenSmiles > (http://opensmiles.org/spec/open-smiles-3-input.html#3.5). I don't > know if CDK conforms though...
Regarding the lower case organic subset, from which the 'c' is derived, the CDK implementation follows the Daylight Depict tool, which sees is as a sp2 carbon. Therefore, is it not conform with the OpenSMILES specification which explicitly limits the lower case organic subset for aromatic atoms. At this moment, the CDK does not fully support OpenSMILES. But note that both SMILES and OpenSMILES assume aromaticity to be detected. Also note that the OpenSMILES only addresses aromaticity of isolated single rings (many drugs actually fall outside this limited scope). The CDK aromaticity perception perceives aromaticity of up to three fused rings. What the CDK does regarding reading of SMILES is represent truely what is read. Excluding an explicit bond order in SMILES means a single or aromatic bond; for both SMILES the bonds should be marked aromatic; because the CDK does currently not have a bond order UNKNOWN, it makes it a single order bond. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
