Noel O'Boyle wrote: > 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.
not sure at all, just trying to figure out what is available and what it all means. > > 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. E > > > >> >> 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
