Noel, thanks for the reply. I thought it was a mistake in my code, so I collected a few of those problematic molecules because I have to deal with them very often (once I didn't notice them and they sneaked into some results, making the synthetic chemists fairly nervous).
When debugging it, I found that the problem seems to be independent from the input format, and I've tried all combinations of data (i.e., 1D, 2D and 3D): >> CC1CCCC[NH+]1C [format: smi] chiral: 2 [ elem: 6] - has no TS config - refs: (1L, 7L, 3L) - chirality fixed: False chiral: 7 [ elem: 7] - has no TS config - refs: (6L, 8L, 2L) - chirality fixed: False >> C[C@H]1CCCC[N@@H+]1C [format: smi, 1D] chiral: 2 [ elem: 6] - has no TS config - refs: (1L, 3L, 8L) - chirality fixed: False chiral: 8 [ elem: 7] - has no TS config - refs: (7L, 9L, 2L) - chirality fixed: False >> [NH+]1(C(CCCC1)C)C [format: mol2, 2D] chiral: 1 [ elem: 7] - has TS config - refs: (2L, 6L, 4294967294L) chiral: 2 [ elem: 6] - has no TS config - refs: (1L, 3L, 7L) - chirality fixed: False >> [N@H+]1([C@H](CCCC1)C)C [format: mol2, 3D] chiral: 1 [ elem: 7] - has TS config - refs: (2L, 9L, 6L) chiral: 2 [ elem: 6] - has no TS config - refs: (1L, 3L, 7L) - chirality fixed: False I remember Geoff fixed some of the problems related to chirality in in rings (with the distance geometry approach, I believe). Unfortunately, even with the latest code from GIT the problem I reported still persists. Let me know what I can do to help fixing the issue. Thanks, S On 04/27/2016 01:42 AM, Noel O'Boyle wrote: > There are some bugs in the stereo perception, and this looks like one. > Was the molecule read in from SMILES? > > It might be worth compiling a list of all problematic molecules you > come across (well, one example of each type) so that a future > developer can fix this. > > Regards, > - Noel > > On 27 April 2016 at 01:29, Stefano Forli <fo...@scripps.edu> wrote: >> Hi all, >> >> I'm trying to enumerate all enantiomers for chiral centers in a given >> molecule, and I'm >> using the following Python code: >> >> org = self.facade.GetTetrahedralStereo(idx).GetConfig().refs >> new = ( org[1], org[0], org[2] ) >> self.chiralSet.append((org, new)) >> >> This code works well most of the times. Problems arise with molecules like >> "CC1CCCC[NH+]1C", in which nitrogen has as a tetrahedral configuration >> defined, but the >> carbon (C1) doesn't. >> >> Is there a better way to deal with chirality and avoid this issue? >> >> Thanks, >> >> S >> >> >> -- >> >> Stefano Forli, PhD >> >> Assistant Professor of Integrative >> Structural and Computational Biology, >> Molecular Graphics Laboratory >> >> Dept. of Integrative Structural >> and Computational Biology, MB-112A >> The Scripps Research Institute >> 10550 North Torrey Pines Road >> La Jolla, CA 92037-1000, USA. >> >> tel: +1 (858)784-2055 >> fax: +1 (858)784-2860 >> email: fo...@scripps.edu >> http://www.scripps.edu/~forli/ >> >> ------------------------------------------------------------------------------ >> Find and fix application performance issues faster with Applications Manager >> Applications Manager provides deep performance insights into multiple tiers >> of >> your business applications. It resolves application problems quickly and >> reduces your MTTR. Get your free trial! >> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Stefano Forli, PhD Assistant Professor of Integrative Structural and Computational Biology, Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112A The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
