Hi all, To summarise, I need to make a decision on how to handle cis/trans stereochem at ring closures in SMILES and I think that Daylight are wrong.
Daylight has the following: (a) C/C=C/1NC1 is the same as (b) C/C=C1NC\1 and (c) C/C=C/1NC\1 The consequences are that (1) conjugated double bonds in a ring cannot be represented by SMILES, and (2) only expert users would know that SMILES a and b are the same. If I were in charge of SMILES, I would require that only the ring closure symbol on the double bond indicated the stereochemistry. Stereo at the other ring closures would be ignored. This would increase the functionality and reduce ambiguity. Specifically (1) conjugated double bonds in a ring would be representable by SMILES, and (2) SMILES b, with its inherent ambiguity, would be regarded as unspecified stereo. So what to do? Some sort of compromise. (1) Well, for starters Open Babel will only write out form (a). (I think this is already implemented, but I will be checking) (2) Where two stereos are specified, Open Babel will ignore the one that is not on the double bond. This will allow the representation of conjugated double bonds in a ring. (3) Where a single stereo is specified, it will be interpreted in accordance with Daylight's ambiguous system. (I would much prefer just to ignore the stereo symbol at a ring closure away from the double bond - it's almost certain that the user will not have understood Daylight's arbitary rule and it will be wrong.) I discussed this to a certain extent on the blueobelisk-smiles list with Bob Hanson and Craig, but I didn't have time/energy to flesh out my disagreement. The core argument presented against what I am suggesting is that this is not what Daylight does. I no longer think this is a valid reason for crippling the SMILES spec in this way. - Noel ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
