Hi Marco, Looks like a bug - thanks for reporting. I've filed a bug report at https://sourceforge.net/tracker/?func=detail&aid=3481603&group_id=40728&atid=428740
If you want to monitor, log in with a SourceForge account and click Monitor. Regards, Noel On 25 January 2012 15:21, Marco <marcolipp...@gmail.com> wrote: > Hi, > > I am encountering a problem when asking OpenBabel to generate an InChI from > a molecule which has an alias bonded through a wedge/hash bond... It seems > to be missing the wedge/bond after expanding the alias... > > Here is an example of what I mean: > > > OpenBabel01241222313D > > 20 21 0 0 0 0 0 0 0 0999 V2000 > -3.2672 1.9552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.4572 0.9403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.9562 -4.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.7871 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.1816 -0.9104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -4.4572 -1.0299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -2.0564 0.9403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0125 -1.9254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.5553 -2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.7662 -1.0597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.9562 -2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.1566 -1.3582 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -3.4342 3.6269 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0334 1.6269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 2.5783 0.6418 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > 5.0000 -1.3582 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > -3.4342 -2.3433 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -1.0334 -4.3433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3674 -4.3433 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > 5.0000 -5.3284 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 1 7 2 0 0 0 0 > 1 13 1 0 0 0 0 > 2 6 2 0 0 0 0 > 3 4 1 0 0 0 0 > 3 11 1 0 0 0 0 > 3 20 1 1 0 0 0 > 4 19 1 0 0 0 0 > 5 7 1 0 0 0 0 > 5 8 1 0 0 0 0 > 5 17 2 0 0 0 0 > 6 17 1 0 0 0 0 > 7 14 1 0 0 0 0 > 8 12 1 0 0 0 0 > 8 18 2 0 0 0 0 > 9 10 1 0 0 0 0 > 9 12 1 1 0 0 0 > 9 19 1 0 0 0 0 > 10 11 1 0 0 0 0 > 10 15 1 6 0 0 0 > 11 16 1 1 0 0 0 > A 13 > OMe > A 15 > OAc > A 16 > OAc > A 20 > OAc > M END > > > The generated InChI is > > InChI=1S/C18H22N2O10/c1-8(21)28-12-7-27-18(16(30-10(3)23)15(12)29-9(2)22)20-17(25)13-14(24)11(26-4)5-6-19-13/h5-6,12,15-16,18,24H,7H2,1-4H3,(H,20,25)/t12?,15?,16?,18-/m1/s1 > > Am I missing something ? > > Thanks ! > > Marco > > -- > View this message in context: > http://forums.openbabel.org/Expanding-aliases-with-wedge-hash-bonds-tp4327511p4327511.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
