Tim and Noel thanks a lot for the info and links. Looks very useful. I didn't know about HOSE codes. It seems hard though to use those to generate a atoms label that you can use in a pdb file (max 4 characters ; since I'm working with 3D structures that would be convenient)
Regarding the symmetry classes I had alreay run into mol.OBMol.GetGIDVector yesterday but from the documentation in http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBMol.shtml#de880e97f2bdf3c90e91375aec12aaf0 I can't figure out how to use it. import pybel smi='COC1=C(C(N)=O)C(C)=CC(C)=N1' mol=pybel.readstring('smi',smi) mol.OBMol.GetGIDVector(???) what kind of argument does it expect? It seems some kind of vector,but what? maybe I'm confusing the python/pybel and c++ worlds. Are there any usage examples to be found on the web? thanks ahead, E Tim Vandermeersch wrote: > 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
