On 9/29/11 10:38 AM, Noel O'Boyle wrote: > "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.
Right. And besides that, with canonical SMILES, it's often necessary to write more than two up/down designations just for simplicity. The resulting SMILES has to be canonical. If you're only going to pick two of the four non-hydrogen bonds in this molecule, which two would you pick? I'm sure you could devise an algorithm that would work, but a simpler approach is to write the up/down bonds on any atom that's not a hydrogen. That way the canonical SMILES is always the same. Note that this isn't "two pairs" of up-down marks. It's just one double bond with all four of the attached atoms marked up or down. Craig > - 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 > ------------------------------------------------------------------------------ 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
