Thanks both of you. 'Got it' -re: CIP/RDkit etc--thanks for guidance--will probably go with Noel's advice 'side-stepping' the issue for now with scripting mol-file generation-(didn't 'see' that I could do that---now I do)--but may have a look at the port issues at some point---and sorry guys will 'post to group' next time instead of a personal 'ping'. Both of your efforts surrounding OpenBabel and Avogadro and opensource facilitates and empowers so much research and coding. Thanks for sharing the 'fruit' of your development. Danni
----- Original Message ---- From: Noel O'Boyle <baoille...@gmail.com> To: Geoff Hutchison <ge...@geoffhutchison.net> Cc: dannihar...@sbcglobal.net; Openbabel-DEV net <openbabel-devel@lists.sourceforge.net> Sent: Fri, February 17, 2012 5:30:25 AM Subject: Re: [OpenBabel-Devel] CDX-and chirality(Sept 2007 last post) 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
