The kekulization code has been replaced in the development version (available from Github). Note that there are also other changes so you should do this with caution.
- Noel On 29 June 2017 at 04:57, Nathan Jenkins via OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net> wrote: > I realize OpenBabel is not designed for dealing with extreme systems, but I > really appreciate offloading some of my work to it. I haven't written a > minimal test case yet, so I can't submit a bug report just yet. Essentially > I am using OBConversion to read protein complexes from PDB-like files with > the standard PDB format in OpenBabel. The reason I say PDB-like is the files > were generated by a homology modeling workflow and I noticed that what > OpenBabel successfully read all had warnings about not strictly following > the PDB standard. When I try loading the groEL complex, I am getting a stack > overflow induced segmentation fault that Valgrind traces to line 733 of > ketulize.cpp. I am on linux and I recently had another program that wouldn't > even compile due to large static arrays. > > Do you think I should try recompiling OpenBabel with -mcmodel=large? Any > other suggestions? I can't really justify too much community service to my > professor at this point in my PhD, so refactoring OpenBabel to use more heap > allocations is not really an option. Eventually my system will be dealing > with millions of OBMol objects managed by my code. Thank you so much for > your help. > > Nathan > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
