On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB <e...@zobio.com> wrote: > > hi, > > I'm looking for some convenient standard atom naming scheme that I > could use for assigning (1H) NMR resonances on a large set of compounds. > > Preferably, atoms that are topologically similar and/or are chemically > and or magnetically equivalent would have similar names (or root names), > for example the protons of a single methylgroup, equivalent protons > of rotating aromatic groups (like PHE/TYR HD/HE). > > My initial thoughts run in this direction: > > * generate cansmi (to be independent of how the input format is specified) > > * name heavy atoms numerically or alphabetically following the smiles string > or > molecular tree from the start, preferably taking symmetries in the molecule > into account (but how?).
OpenBabel has symmetry classes which might be an initial starting point. See OBGraphSym and: http://timvdm.blogspot.com/2009/09/symmetry-classes-how-to-get-them-and.html > * name the hydrogens after the attached heavyatom. > > First and last point are trivial I guess, but the middle point seems to > be quite tricky. I'm probably not the first with this problem, so if anyone > knows software that does something similar or has suggestions how to approach > this, I would be very grateful. > > kind regards - Eiso > > > > > > > > > > > > ------------------------------------------------------------------------------ > 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 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ 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 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
