On 16 February 2011 16:38, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> IsSetupNeeded() caused me to lose a day or so searching for a segfault in >> Confab. In the end, I figured out what the problem was (Setup wasn't being >> called) and so I modified the function to always return True, as it's >> essentially a test for molecular identity that doesn't always work. Sooner >> or later it's going to fail, and a failure here means a difficult to >> diagnose segfault halfway through processing a large number of compounds. > > I respectfully disagree completely. Confab is *exactly* the reason > IsSetupNeeded() is needed. :-) > > Confab generates conformers -- so you want to be able to do atom typing, > formal charges, partial charges, etc. exactly *once* per molecule. Then you > want to run the forcefield a lot on your different conformers. You don't need > to re-do "setup." > > If you look through Paolo's changes, they make a lot of sense. In fact, it's > a pretty solid test for molecular identity. > > If you're getting segfaults by *ANY* part of the Open Babel code, it needs to > be reported and tested. I'm still trying to see if I can reproduce Andrew > Dalke's reported segfault in fingerprints from last week.
Can we postpone this discussion for next time we meet, otherwise I feel like it will take some long emails to go over the philosophical and technical reasons why I'm right and everyone else is wrong, and even then I might lose the argument. :-) > That's my $0.02, > -Geoff > ------------------------------------------------------------------------------ > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > Pinpoint memory and threading errors before they happen. > Find and fix more than 250 security defects in the development cycle. > Locate bottlenecks in serial and parallel code that limit performance. > http://p.sf.net/sfu/intel-dev2devfeb > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
