> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such > way that the bond orders are no longer dependent on the way the molecule was > entered? For example, the two smiles representations of the indole ring, > N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12, lead to differences in the internal > bond orders and this has influence on the aromaticity perception.
Are you sure you're using 2.3 release? I just tried these two smiles and asked for canonical SMILES and got the same (correct) answers. We fixed a *lot* of Kekulization bugs prior to release, so please make sure you're using 2.3 branch or 2.3.0 release. [ghutc...@geoffh-desktop] openbabel: echo "N1C=CC2=CC=CC=C12" | babel -ismi -ocan c1ccc2c(c1)[nH]cc2 [ghutc...@geoffh-desktop] openbabel: echo "N1C=CC2=C1C=CC=C2" | babel -ismi -ocan c1ccc2c(c1)[nH]cc2 Thanks, -Geoff ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
