Hi, On Mon, Aug 6, 2012 at 12:24 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > Even more unforunately, it's not possible to access most of the stereo > functionality from anything but C++. This is due to the use of nested > classes for the stereo config, which we realised after-the-fact is not > supported by SWIG. I've tried workarounds but I'm running short of > ideas. > > Geoff's idea to build the structure based on SMILES seems like a good > way to go for the moment.
Since this issue has come up several times I've added support for this. See commit r4973 & r4974. An example test script can be found here http://moldb.net/timvdm/openbabel/obstereo.py Tim > - Noel > > On 31 July 2012 03:59, Geoff Hutchison <ge...@geoffhutchison.net> wrote: >> Unfortunately, Noel (the best person to answer this) is on holiday and >> changing jobs shortly. My best suggestion would be to start with SMILES >> (i.e., if you have the molecule/bond info, generate SMILES). This should set >> the stereochemistry correctly. >> >> Using the stereo classes is possible, but I don't have much experience using >> them directly. >> >> -Geoff >> >>> I've been using the Python openbabel module to create atomic coordinates >>> based on molecule/bond information for mostly modified amino acids; this is >>> all working fine except that I'm struggling to set the stereochemistry (and >>> generate, for example, the correct cis/trans peptide bonds). >>> >>> I was hoping someone has some examples (for the openbabel Python module) to >>> set cis/trans and tetrahedral stereochemistry and is willing to share >>> these; I haven't been able to find anything online. >> >> >> ------------------------------------------------------------------------------ >> 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-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ > 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-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ 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-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
