When I try obgen on OCC(=O)[C@@]1(O)CC[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H]2CCC2=CC(=O)CC[C@]12C)F
I get a message WARNING: damped steplength 16.7257 to 2.25803 on stdout rather than stderr (so dumped into the SDF file making it invalid) If I edit the SDF file to remove that message, and run obprop, I find that the generated structure is OCC(=O)[C@@]1(O)CC[C@H]2[C@]1(C)C[C@H](O)[C@@]1([C@@H]2CCC2=CC(=O)CC[C@]12C)F (IE the wrong chirality at the second, fifth and sixth chiral carbons) For comparison, obgen from the released 2.3.1 produces something which obprop-svn4747 reports as CC(=O)[C@@]1(O)CC[C@H]2[C@]1(C)C[C@@H](O)[C@@]1([C@@H]2CCC2=CC(=O)CC[C@]12C)F (IE the wrong chirality at the fourth chiral carbon) I realise that steroids are nasty test cases, but they are annoyingly pharmaceutically relevant Tom ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
