On Die, 2009-05-26 at 18:58 +0200, Egon Willighagen wrote: > On Tue, May 26, 2009 at 6:12 PM, Noel O'Boyle <baoille...@gmail.com> 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 >
Ok, I see. I don't think that it will be a big problem, as we decided to store the molfile in the db as well, because most real world scenarios would be to load compounds from SDFiles. The SMILES part is mainly for students to play around, but they can use the JChemPaint too. (I realize that it's hard to write an app suitable for both industry and education). Internal representation is molfile, so most functions (mainly descriptor calculation and modelling) will work well, I hope. On Die, 2009-05-26 at 16:51 +0100, gilleain torrance wrote: > That said, both will be drawn with a circle in the center if the > renderer model has setShowAromaticity=true. I don't think there is a > way to show aromatic circles AND the double bonds in aromatic > systems... Maybe you misunderstood me. I don't want a ring drawn inside, but the alternating double bonds ala Kekule. What made me perplex was that even with setShowAromaticity=true or with the CDKStyle the ring is not drawn. Ok thanks again für your answers Greetings Sebi ------------------------------------------------------------------------------ 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 Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
