Hi, On Wed, Mar 3, 2010 at 4:41 PM, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: > > On Mar 3, 2010, at 10:31 AM, Noel O'Boyle wrote: > >> * test/graphsymtest.cpp: There are still some cases were this test >> fails. However, it mainly has to do with N atoms becoming aromatic >> and getting an extra H atom. I'm not sure what's the best solution >> here... >> >> Could you file a bug about this? This is the single biggest problem >> remaining. > > How is this a bug? This is the test case: > CC1=CN(C(=O)NC1=O)[...@h]2c[c@@H]([...@h](O2)CNCC3=CC=CC=C3)O
It's not really a bug AFAIK. You just can't expect the same symmetry classes for the two structures using the current implementation. > When I paste this into ChemDraw, I get the attached PNG -- with added H. This > is the correct Kekule structure, which is also what OB assigns. The correct > SMILES should be: > Cc1cn(c(=O)[nH]c1=O)[...@h]1c[c@@H]([...@h](O1)CNCc1ccccc1)O > > This string passes the graphsymtest. There are other kekule errors, but this > isn't one. Should we change this in the unit test (i.e. use the new smiles string)? Do you mean the crashes in expand_kekulize? These are often seen when opening pdb files (from Avogadro for example). Cheers, Tim > -Geoff > > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
