On Wed, Mar 27, 2013 at 02:04:00PM -0700, Craig James wrote: > Reinis Danne <rei4...@gmail.com> wrote: > > > > I think it was the thread where I mentioned I'm working on > > > kekulization algorithm using graph theory (maximum matching). It > > > has been quite some time when I last looked at that code and it > > > is not yet usable. > > > > > I don't know if this overlaps with your work, but I spent a fair amount of > time on the aromaticity-detection algorithm and improved it by orders of > magnitude. See the comment in kekulize.cpp around line 887 -- copied below. >
Still there are situations (even not that complex ones) where the current algorith fails to find correct kekule form of aromatic system and that is one of the main reasons I'm looking into another algorithm. Another issue is that we are getting heap overflows with proteins of moderate size. I wrote some patches to reduce heap usage by the existing algorithm and they are in master branch, but it only postpones the problem until one tries to work with even larger molecules. Alternative solution would be to rewrite existing algorithm in non-recursive form. Also, I'm looking into this, because it is just interesting :) I'm using boost's graph theory library. I think it is not worth it to reimplement basic graph theory algorithms and the boost dependency is completely justified. I'll clean up the code and put it on GitHub when have a bit of time for that. Reinis ------------------------------------------------------------------------------ Own the Future-Intel(R) Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
