Hi Nick, On Thu, Mar 17, 2011 at 4:54 PM, Nick Vandewiele <nickvandewi...@gmail.com> wrote: > I found strange behaviour of the CDKConstants.VISITED flag after running the > SMARTSQueryTool on cyclic species. > -Normal behavior for linear alkanes such as n-decane:
<snip> > The VISITED flag returns 'false'. > > -Non-consistent behavior for cyclic species, like benzene: <snip> > The VISITED flag returns 'true'... The VISITED flag is used by some algorithms like ring system detection, which is used itself for aromaticity detection. I guess this may be needed for some SMARTS. Without looking at the code, I can only guess why atoms are not visited for alkanes, but if that difference is consistent, it sounds to me to have to do with ring detection, which indeed uses this flag. But these flags are used internally, also, btw, making it impossible to run more than one algorithm on one class, and should not be relied upon to be persistent. Rajarshi's solution should be such for such cases instead. Grtz, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
