On a somewhat related note, why does the atom type set aromaticity. Shouldn't this be done via the perception class?
On Tue, Oct 4, 2011 at 8:36 PM, Rajarshi Guha <rajarshi.g...@gmail.com> wrote: > 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 > -- 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
