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
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