Looks like a bug. Not sure how I missed this one. I'll look into it asap. - Noel
On 29 November 2011 11:17, JP <jeanpaul.ebe...@inhibox.com> wrote: > Using OpenBabel 2.3.1, on Ubuntu Linux 10.10 > > Using the attached *seemingly unsuspect and correct* sdf file - zzz.sdf. > > Converting this file to smiles: > > $ obabel zzz.sdf -osmi -Ozzz.smi > 2 molecules converted > > Gives us the expected and correct result: > $ more zzz.smi > C[C@@H](N)C(=O)O Ala1 > C[C@H](N)C(=O)O Ala2 > > Adding hydrogens to the original sdf file: > > $ obabel zzz.sdf -osdf -OzzzH.sdf -h > 2 molecules converted > > Now converting the H-added sdf file to smiles: > > $ obabel zzzH.sdf -osmi -OzzzH.smi > 2 molecules converted > > STEREO INVERTED:: (!!!) > > $ more zzzH.smi > C[C@H](N)C(=O)O Ala1 > C[C@@H](N)C(=O)O Ala2 > > Any ideas why this happens? This is somewhat unexpected behaviour. > > > - > Jean-Paul Ebejer > Early Stage Researcher > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
