Dear Deepak, On Wed, Jun 16, 2010 at 8:52 AM, <deep_ku...@imtech.res.in> wrote: > Thanks for replying. I am using cdk-1.0.3.jar.
Have you considered using CDK 1.2 or perhaps even the CDK 1.3 development version? Also, what is the code you use to run CDK functionality? That is, what does the relevant source code of packageWebCdk.java look like where you call the 3D model builder? > i dont understand what is HOSE code. A HOSE code is a line notation for an atomic environment. The CDK 1.0 code you are using, uses it for looking up the proper 3D environment for that atom. But, it is unable to find it in the database... I think this is caused by the missing negative charge on the oxygen, but that is just a guess. More information on the HOSE code generation is found in this JavaDoc: http://pele.farmbio.uu.se/nightly-1.2.x/cdk-javadoc-1.2.5.git/org/openscience/cdk/tools/HOSECodeGenerator.html Anyway, I strongly suggest to move to CDK 1.2. CDK 1.0 is outdated, has many bugs that are fixed in CDK 1.2, and the problem you encounter may just be one of those. Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
