Have you tried the development version? This has been rewritten. On Fri, 16 Nov 2018, 00:19 Stefano Forli <fo...@scripps.edu wrote:
> Hi, > > I've found a series of molecules that trigger what looks like a bug but I > want to make sure there isn't something clearly wrong with the structures, > before reporting it. > > The molecules look fine when inspecting them in 3D (Pymol), but OpenBabel > (both 2.3 and 2.4) parse the structures removing entirely the aromaticity > information. > > $ obabel ZINC000008616812.mol2 -ocan > C[C@@H]1CC[C@@H]([C@@H]2[C@@H]1[NH2+][C@@H](C)CC2=O)Cl ZINC000008616812 > 1 molecule converted > > $ obabel ZINC000000119428.mol2 -ocan > Cl[C@@H]1CC[C@@H](CC1)N1NNN[C@@H]1[C@H]1C[NH2+][C@@H]2[C@@H](C1=O)CCCC2 > ZINC000000119428 > 1 molecule converted > > I don't think in this form the 4-pyridone is aromatic, but I still think > there's something wrong with the way the valence information is lost when > parsing the structures. > > Any clues? > > Thanks, > > S > -- > > Stefano Forli, PhD > > Assistant Professor > Dept. of Integrative Structural > and Computational Biology, MB-112A > The Scripps Research Institute > 10550 North Torrey Pines Road > La Jolqla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > fax: +1 (858)784-2860 > email: fo...@scripps.edu > http://www.scripps.edu/faculty/forli/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
