Hi Paul, > is there a way to include results from obchiral into the smiles strings > generated by babel? One can highlight chiral atoms inside smiles using > an asterisk when one does not wan't to give the absolute configuration. > > e.g. CCC*(C)(O)C(C)C, instead of c...@](C)(O)C(C)C or CC[C@@](C)(O)C(C)C > > How can I get the first string when converting from a mol file?
As Geoff says, the SMILES you are asking for is invalid (the '*' is actually a valid atom, so you've added an atom to the molecule), but if you have a specific reason to do this, and you're using Linux or a Mac (or you have something like Cygwin on a PC), you could combine OpenBabel with traditional tools like sed: $ echo "c...@](C)(O)C(C)C" | babel -i smi -o can | sed -e 's/\[C@@*H*\]/C*/g' CCC*(C)(O)C(C)C Craig ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
