On Nov 22, 2010, at 6:24 PM, Craig A. James wrote: > It appears that OpenBabel retains the original single/double bond assignment > and uses that to determine aromaticity of the remaining part of the molecule > after atoms are deleted. But depending on the original Kekule assignment of > bonds, the bond that's common to both rings might be single or double. Once > you remove the rest of the benzene ring, the remaining ring may be either > aromatic or not aromatic.
Oh, right. That makes much more sense. >From Hans's original message: > removing the six-membered benzene ring from the second indole representation > leads to 'saturated' pyrrole (only one of the two C-C bonds has a bond order > of 2) and therefore not longer aromatic (see attached figure). One big problem for Open Babel right now is that it (and many other cheminformatics toolkits) are not designed well enough for editing. The model is "read in a molecule and we'll give you a representation." We run into similar problems with Avogadro and that's one reason I've tried to improve the OB code in this manner, but it's clearly not perfect. In principal, using OBMol::BeginModify() and OBMol::EndModify() will perform new perception as needed, but there are probably still bugs, since this receives much less testing than other aspects of the code. In short, please contribute bug reports and unit tests. :-) While the bond orders will be given by the original Kekule assignment, the bonds (and atoms) will still be marked as aromatic. So the best solution for code like Hans is to delete the atoms, then make a pass through remaining bonds to mark as aromatic and pass through Kekulize again. -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
