It looks like the problem is in lines 404-405 in SmilesGenerator. It appears that even if useAromaticityFlag is set to TRUE, the code performs atom typing as well as aromaticity perception. In fact, the atom typing step messes up the aromaticity flags on the atoms and as a result the resultant fragment comes out with no aromaticity.
Commenting out these two lines (and ensuring that useAromaticityFlags = TRUE) outputs the fragment in aromatic form. As far as I can tell, performing aromaticity perception in this block is invalid - since the flag says to use the pre-exisiting aromatic flags. But I'm not sure of the role of atom typing in this block On Thu, Sep 8, 2011 at 4:08 AM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > On Thu, Sep 8, 2011 at 9:33 AM, Martin Guetlein > <martin.guetl...@googlemail.com> wrote: >>> It might be solved by using SmilesGenerator.setUseAromaticityFlag(true)... >> >> setUseAromaticityFlag(true) is already part of the code, but has no effect >> on this example. > > This was exactly why I had not replied yet... I had not had enough > time to read the details... :( > > Maybe it has to do with the final structure not being a ring... a > quick scan of the source code, seems to rule out that idea... I'd have > to run a full debug for this... > > Please file a bug report. > > 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 > > ------------------------------------------------------------------------------ > Doing More with Less: The Next Generation Virtual Desktop > What are the key obstacles that have prevented many mid-market businesses > from deploying virtual desktops? How do next-generation virtual desktops > provide companies an easier-to-deploy, easier-to-manage and more affordable > virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
