On 18 August 2010 15:47, Eiso AB <e...@zobio.com> wrote: > > 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)
Well, you could just create a one-to-one mapping between the HOSE code and a 4-letter label. If you have more environments, then the 4 characters won't help in any case. > 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? Hmmm...are you sure that's what you want to do? The symmetry labels will not be the same between different molecules, whereas the circular fingerprints would be. Anyway, these are most easily used through a GraphSym object (see http://openbabel.org/dev-api/classOpenBabel_1_1OBGraphSym.shtml). So you need to pass in a vector unsigned int to GetSymmetry. In python, try openbabel.vectorUnsignedInt(). > > 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 > ------------------------------------------------------------------------------ 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
