Hi Yannick, I'm a bit confused by your question. What exactly are you trying to do? What results are your trying to visualise?
> Given the fact that there is no unique way to index atoms in a molecule, it has been very challenging for me to visualize the results and > evaluate them Canonical labelling provides a unique index of atoms and bonds. > Is there a way to add atom indexes in the resulting SDF file so that the atoms can be easily mapped no matter what structure viewer I use? The atom indexes in the SDfile are ordered they are in the molecule - all cheminformatics toolkits should have this invariant. Thanks, John Regards, John W May john.wilkinson...@gmail.com On 30 May 2015 at 02:59, Yannick .Djoumbou <y.djoum...@gmail.com> wrote: > Hi all, > > I have been doing some work with CDK that returns among others some atom > indexes. Given the fact that there is no unique way to index atoms in a > molecule, it has been very challenging for me to visualize the results and > evaluate them. Is there a way to add atom indexes in the resulting SDF file > so that the atoms can be easily mapped no matter what structure viewer I > use? More realistically (??), is there any viewer that reproduces CDK's > structure/indexing ? > > Thank you for your consideration. > > Regards, > > Yannick > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > >
------------------------------------------------------------------------------
_______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
