To avoid multiple threads, let's move this over to the opensmiles list. On 2 March 2017 at 20:31, Andrew Dalke <da...@dalkescientific.com> wrote: > On Mar 2, 2017, at 20:34, Craig James <cja...@emolecules.com> wrote: >> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that >> the "organic subset" are only allowed outside of brackets if they're in >> their normal lowest-valence state. Actually, now that I read it, it's not >> well written and has room for (mis)interpretation. The phrase that I think >> applies in OpenSMILES is: > > My understanding of Daylight SMILES is that when the explicit valence based > on the bonds is higher than the maximum natural valence then the deduced > hydrogen count is 0. > > For example, quoting > http://www.daylight.com/meetings/summerschool98/course/dave/smiles-intro.html > : > >> In practice, one chemist might represent nitromethane as C[N+](=O)[O-] with >> a nitrogen of valence 3 in a charge-separated structure while another might >> represent it as CN(=O)=O with a neutral 5-valent nitrogen. Which SMILES is >> correct? Both are. > > > > > On Mar 2, 2017, at 20:34, Craig James <cja...@emolecules.com> wrote: >> If you can say, "It's obvious ...", and this is a feature everyone would >> like, then the OpenSMILES spec could be changed. > > I think it should be changed. > > Andrew > da...@dalkescientific.com > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel
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