Hi Danni, The CDK format stores stereochemistry using the Cahn-Ingold-Prelog system. *sigh*
Unfortunately, Open Babel has no code for interpreting or generating CIP symbols. The first step in adding support would be to port the CIP code from RDKit or so to Open Babel. I'll look into it, but that's probably not trivial...if I were you, I'd try to script ChemDraw to save the files as Mol files (where the stereochemistry is defined relative to the order of the atoms in the file). - Noel On 17 February 2012 02:33, Geoff Hutchison <ge...@geoffhutchison.net> wrote: > No, there is not yet support for grabbing all stereochemistry from CDX files. > In the 2.3.x effort, the stereochemistry code was completely rewritten. > > If you are considering looking at the code, I suggest posting to the list, as > others (particularly Noel O'Boyle) can probably help. > > -Geoff > > On Feb 15, 2012, at 12:00 PM, dannihar...@sbcglobal.net wrote: > >> Geoff----I see a post back on Sept 11 2007 re: loss of chirality info in >> converting between CDX to 'other formats capable of capturing >> stereochemistry'. I still see this an issue in V 2.3.1? Am I missing >> something ---this hasn't been patched? I was going to start to look at the >> code underlying this conversion---but I figure in 2012 this must have been >> 'fixed'. Am I missing something on 'flag specification'? I haven't tried >> this particular version at from the C++ level ---just ---command line. >> Finally thanks for all your development efforts ---powerful tool ---make use >> of it at the C++ level each and every day. Danni > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
