Geoffrey Hutchison wrote: > > On Oct 23, 2009, at 11:03 AM, Craig A. James wrote: > >> I've now got a new version of expand_kekulize() in kekule.cpp, it >> solves a fullerene correctly in a few milliseconds. There's still a >> lot of work to do on the details, and once I have the performance >> right, we need to correct some problems in the chemistry. > > Do you think some of this code can be backported to 2.2.x? I'm wondering > if it's worth a small 2.2.4 release.
As far as I know, the code in kekulize.cpp hasn't changed much for a long time, except for changes I checked in a couple months ago that introduced the performance problem in the first place. The changes are confined to that one file (plus declarations in mol.h), so it should just drop in to 2.2.x. The problem is that I don't have any good before/after test cases to see if I've screwed something up. I guess I could use the 10,000 molecule sample set and run it through babel with/without my changes and compare the files. That would be a start... I have just a small amount more work to do before kekule.cpp is ready to check back in. It has to do with molecules like this: c1ccc2c(c1)c1cccc3cccc2c13 http://depict.emolecules.com/cgi-bin/mymol/depict.cgi?smiles=c1ccc2c(c1)c1cccc3cccc2c13 It has four rings, all aromatic atoms, but one of the rings is not aromatic (even though every atom in that ring is aromatic). It violates the assumption that "a ring is aromatic if all its atoms are aromatic." A ring is actually aromatic only if all of its *bonds* are aromatic. Craig ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
