"As far as I know in SMILES notation every double bond is specified with just ONE pair of slash/backslash"
That's not quite correct. One pair of slashes is sufficient, but more may be used. Open Babel writes out as many as possible as it makes things clearer (explicit is better than implicit). So if there's one "up", then there's a corresponding "down" (unless the down is a H). For example, "obabel -:C/C=C(Br)\I -osmi" gives "C/C=C(/Br)\I". They are identical, but Open Babel gives the Br gets an explicit "up" bond. - Noel On 29 September 2011 17:24, green69 <gcinci...@gmail.com> wrote: > Hi guys! > > I have the following molecule in smiles format: > [O-]S(=O)(=O)c1ccc2NC(=O)\C(=C3/Nc4ccccc4C3=O)c2c1 > > When I canonize it with openbabel I obtain the following: > O=C1Nc2c(/C/1=C\1/Nc3c(C1=O)cccc3)cc(cc2)S(=O)(=O)[O-] > > The molecule is not very strange and it has just ONE double bound over which > a certain regio-isomery is defined. > In the original SMILES I have ONE pair of "slash/backslash" that define the > specified regio-isomery. When I use openbabel (v.2.3.0) to convert the > string into canonical I obtain a SMILES with TWO pairs of "slash/backslash" > symbols to specify just ONE double bond. > As I don't have experience with the "canonizator" of openbabel I need help > to understand what's going on here. As far as I know in SMILES notation > every double bond is specified with just ONE pair of "slash/backslash". As > in the canonical form we loose this 1:1 correspondence, the human > readability is lost. SMILES is a great molecular representation exactly > because it can be parsed by computers but at the same time can be easily > read by chemist. > Does anybody know if this is a bug or a "normal" behaviour of openbabel > canonizer? Please, could anybody explain me what's going on in this case? > > Thank you in advance! > > -- > View this message in context: > http://forums.openbabel.org/very-strange-canonical-SMILES-BUG-or-normal-behaviour-tp3856542p3856542.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
