Hi, This is yet another question on aromaticity detection. The Hueckel detection in 1.4 seems to be rather strict with rings including heteroatoms: * CCN1CCN(CC1)c1cc2n(cc(C(O)=O)c(=O)c2cc1F)C1CC1 (see https://apps.ideaconsult.net/data/depict?search=CCN1CCN%28CC1%29c1cc2n%28cc%28C%28O%29%3DO%29c%28%3DO%29c2cc1F%29C1CC1&smarts= ) * CNc1cnn(-c2cccc(c2)C(F)(F)F)c(=O)c1Cl (see https://apps.ideaconsult.net/data/depict?search=CNc1cnn%28-c2cccc%28c2%29C%28F%29%28F%29F%29c%28%3DO%29c1Cl&smarts= )
I know that there is no common algorithm for detecting aromaticity, and that there are examples where chemists disagree. However, considering these compounds, the chemists in our project (as well as Open Babel, PubChem and Cactvs (see above links)) do think that the rings should be aromatic. Can I change the arom detection behaviour? Is there an alternative to the CDKHueckelAromaticityDetector? The SmilesParser#isPreservingAromaticity() method does not help me, as we create new compounds with reactions using the ambit-smarts library, and arom detection has to be applied to the products. Kind regards, Martin ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
