[Open Babel] Babel on Extreme Systems

[Noel O'Boyle]

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

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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