On 12/07/2010 17:45, Tim Vandermeersch wrote: > On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov > <igor.v.filip...@gmail.com> wrote: >> Is there any way to set atomic labels in openbabel to non-existent >> elements - i.e. X, Y, R1, R2, R3... ? >> >> So far I see only SetAtomicNum to specify atom type, but nothing to set >> the atomic label to something like "R1". > > You can use AliasData for this.
Currently AliasData is essentially an alternative representation of a real structure, as defined by SMILES in superatoms.txt. There is the occasional * representing an unspecified atom, but it does not extend much further towards Markush structures. It would be nice to take it further, but it requires some thought. For instance, should molecules in OB should be required to have chemical meaning, rather than being just being essentially images? Or would descriptions like, "an electron withdrawing group" would be useful?. Using SMARTS rather than SMILES in superatoms.txt goes a long way towards Markush structures but is not completely general. I'm afraid I am not familiar with the way other software handles this. Chris ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
