On 28/06/2011 01:02, A. Heifets wrote: > Any obvious idea why the following file causes a segfault with "obabel > -isdf junk.sdf -osdf -Ofoo.sdf"? It's something to do with the R > groups because, if I replace them with 'C', the file works. Is there > a way to skip generating output instead of making OpenBabel segfault?
This is related to your bug report #3325452. The comments I made on it do not seem to made it on to SourceForge. I'll try again, but the gist is that the development code no longer segfaults with R groups. I can see why your file has the name "junk.sdf". You could try the -r option - Remove all but the largest contiguous fragment. With this file the 5 fragments with R groups (one of them miles away) would be eliminated. But I don't think this prevents the segfault and neither does using -o nul. You would probably have to build the development code. For Windows, I could provide a compiled version. ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
