I don't know how obgrep works, but similar functionality in obabel works like this:
C:\Users\noel>obabel methane.sdf -osmi -s "C" C Note that using single quotes fails (at least on Windows). - Noel On 11 June 2013 15:44, Pascal Muller <pascal.jm.mul...@gmail.com> wrote: > - Sorry, forgot to cc the list - > > > Hi, > > >> >> >>> >>> Usually, I use obgrep (Open Babel 2.3.2) with smiles files, but today I >>> tried with an sdf - and it doesn't work. There is no match, and no error >>> message (e.g. >>> obgrep 'C' methane.sdf >>> gives no output, as if there were no match. Tried with and without H in >>> the sdf). >> >> >> Forgive me if this is too simple, but are sure there are aliphatic carbons >> in your SDF? The SMARTS "C" won't match aromatic carbon atoms. > > > Sure :) > >> >> >> If that's not the case, then maybe you could attach your SDF. Otherwise, >> we're just guessing. > > > No obgrep query is working with any of my sdf, e.g. methane structure, but > these queries are all working with the corresponding smiles files. E.g. > methane.sdf is: > > > methane > OpenBabel06111316402D > > 1 0 0 0 0 0 0 0 0 0999 V2000 > 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > M END > $$$$ > > > > Regards, > Pascal > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-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 Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
