On 27 September 2010 20:39, Noel O'Boyle <baoille...@gmail.com> wrote: >> By moving the stereo spec back onto the double bond itself, all the problems >> go away. > > Sounds like a good idea but I don't want to get into discussions on > alternative syntax here - we have enough to discuss already :-) > >> Back to the present... the immediate problem of what to do for OpenBabel >> really has two parts: parsing SMILES and printing SMILES. I think they are >> two different problems. >> >> For printing SMILES, I totally agree with your plan: Only print out example >> (a). > > Right. > >> But for parsing SMILES, I think we should use the "either bond, or both, but >> if both they must agree". It just doesn't seem like a good idea to ignore >> errors. If the stereochemistry symbols disagree then there's a 50/50 chance >> you're picking the wrong one. > > My point is that if you stick to "if both they must agree" then you > have the problem of representing conjugated double bonds in a ring. I > think you are saying that you believe this is the lesser of two evils. > This is, admittedly, an uncommon occurrence.... > > Ok. So, after emitting a warning I guess I should make it stereo > unspecified? (the alternative is to take the stereo at the double > bond.)
The following blog post summarises the handling of this stereo in Open Babel: http://baoilleach.blogspot.com/2010/09/are-you-on-my-side-or-not-its-ez-part.html - 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
