On Thu, Aug 12, 2010 at 8:50 PM, <ma...@ebi.ac.uk> wrote: > One more thing, in the example I sent, the one ring that does not get > aromaticity detected thus ends up as a ring with only single bonds. I > though that in particular was not a desirable effect.
Yes, that was discussed this week. Basically, the SMILES does not define where the double bonds are, for which we have a partly working DeduceBondSystemTool... but that algorithm does not work flawlessly... see the thread this week, and a few code clean up patches up for review (hint, hint :)... One bad attempt I made this week, was to use a SINGLE_OR_DOUBLE bond, as that comes pretty close... but that horribly failed (again, see the thread on cdk-devel)... So, I might still attempt to just set the bond order to *null*, which we use as UNKNOWN... that would actually reflect what's in the SMILES most precisely... Thus, agreed... setting it to SINGLE is just bad, but historical too... only until recently, we could not set the bond order to null, short for UNKNOWN... Now, the advantage of having it set to SINGLE_OR_DOUBLE or the more appropriate UNKNOWN, would be that we can guide the DeduceBondSystemTool, to only analyze bonds with undefined bond orders, instead of all bonds, which is a much harder problem... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) 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 ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
