This problem with plugins loaded from the plugindefines.txt has been causing issues for me too, mainly when pybel sporadically complains that the list of descriptors is garbage.
I've tried tracking it down, without much success. It seems to be a problem with all plugins that are loaded from a file using OBDefine in loader.cpp, not just the SMARTS descriptors. (Also, the SMARTS descriptors loaded manually at the end of smartsdescriptors.cpp look fine to me.) I think the problem is to do with plugins using const char* pointers for the ID, description etc. These pointers are created from std::strings using .c_str() in MakeInstance, and I think maybe the original string is being destroyed or going out of scope, hence the char* pointer becomes garbage. The only problem is, as far as I can tell, loader.cpp looks after the strings just fine so they shouldn't be destroyed. In loader.cpp, OBDefine reads the relevant strings from plugindefines.txt, then copies them into a private member vector _text, to ensure they stay around for the lifetime of the OBDefine instance. The strings in _text are then used to call MakeInstance on SmartsDescriptor, PatternFP, CompoundFilter, etc. which uses c_str() to create a pointer to the string in memory. Right after the descriptors are created, accessing GetID() returns it fine. But at some later point this becomes garbage, even when the OBDefine instance is still around and the strings in OBDefine's _text are still completely fine. If the original string hasn't been destroyed, one other thing that could invalidate the c_str() result is if a non-const member function of the string is called. I can't see this happening anywhere either though. Matt On 2 Jan 2014, at 21:32, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: >> Can you figure out a minimal plugindefines.txt that still causes the problem? > > Good point. I'm now seeing that the main issue is with SMARTS descriptors. > I'll see if I can find the problems later tonight. > > Thanks, > -Geoff > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
