On Mon, Jun 21, 2010 at 6:12 PM, Geoffrey Hutchison <[email protected]> wrote: >> Is anyone familiar with the SSSR code? Geoff's name is in the file but >> I don't know if there have been many ring perception bugs in the past. > > I think there was one. I believe some parts of the code have also been > contributed by Joerg Wegner through his JOELib project. Those should be > documented. > > I agree with your remaining comments. I've been meaning to update parts of > the ring perception code with similar ideas to what you discussed in your > blog post. I just have not had the time to sit down and code this, and > there's been other low-lying fruit as far as bug-fixes.
Do you mean the SSSR superset? Or something regarding the performance/size limit? > So if you've got the time, please feel free to give it a crack! The bugfix is in svn trunk. In the RemoveRedundant function, the last found ring was always removed. Even if the number of rings in the ring set only contained frj rings. I'll see if there are other bugs like this on sf. I now have a general idea of what most functions are doing but we seem to detect ring closure bonds twice. The first is contained in OBBond::IsClosure(), it sets a flag to not run again though. The second version is in FindRings (src/ring.cpp). The second does a backtrack marking atoms and bonds with SetInRing. The first only sets the OBBond::IsClosure flag. OBMol::FindSSSR (src/ring.cpp) mixes both... OBBond::IsClosure should just call OBMol::FindSSSR to set the IsClosure property... (I'll try to change this and test) Tim > -Geoff > > ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
