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
