> It would be nice if I had the ability to write (canonical) SMILES strings > without any bond order information, as a "round trip" to another format > (say, .xyz with gen3D) may cause this information to be lost and I end up > with different strings for the same molecule. For example, > [NH3][CH2][C](=O)=O is the same molecule as [NH3][CH2]C(=O)O . >
I think what you're saying is, "I would LIKE these two molecules to be interpreted as the same molecule." The rules of SMILES say that those are two different molecules. SMILES is a formal language with specific rules that don't allow alternate interpretations. > If there was a way to delete bond order information in the OBMol object, > I'd be happy with that too, as it would allow me to write the string I > want. Thanks! > That's not so easy. You'd probably need to write your own program using OpenBabel that erased certain types of infomation (bond order) and rationalized charge and H-count so that all atoms were neutral, then wrote out the SMILES. The problem is that the various parsers go to a lot of trouble to preserve the input molecules exactly as specified. Craig
------------------------------------------------------------------------------
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
