I note that the current StripSalts() tries to retain various flags. Perhaps some are invalid as you say. Does it still fail if you comment out "_flags = tmpflags; "?
- Noel On 3 November 2010 18:34, Hans De Winter <hans.dewin...@silicos.com> wrote: > All, > Doug Houston kindly pointed me to a situation in which Sieve was crashing > when the program was run on an input file that contains counterions in > combination with filter criteria that use SMARTS pattern matching functions > (in particular, the LOGS and LOGP filters). I've attached one of Doug's > molecules for convenience. The command that he used was: > sieve --in 9SPH1-198-630.sdf --filter filter.txt --pass passed.sdf > The 'filter.txt' file contained a "LOGS -5 *" filter line. > The problem is repeatable and also occurs on other molecules with > counterions. Sieve does not crash when the "--salts" commandline option is > used, or when other filters, like the MOLWT filter, are used. > I spent some time trying to identify the cause of this crash, and came to > the conclusion that it has to do with the combination of first calling the > OBMol::StripSalts() method, followed by calling the OBSmartsPattern::Match() > method. However, I still do not completely understand the exact reason for > this segmentation fault, but when I replace the OBMol::StripSalts() method > call within Sieve by an alternative function that does exactly the same as > the original OBMol::StripSalts() method, then a crash seems to be avoided. I > guess that the OBMol::StripSalts() method modifies the original molecule in > such a way that some kind of inconsistencies are introduced in the > connection table (?) which lead to a crash of the system when > the OBSmartsPattern::Match() method is subsequently called. > I've attached the code of the 'StripSalts' replacement function that does > not lead to a crash. If you all agree, I could use this code to correct the > existing OBMol::StripSalts() code, unless one is willing to have a look at > the OBMol::StripSalts() code and identify the exact source of the error. > This would be a less pragmatic fix but maybe nobody has time to have a look > at this. > Please let me know your thoughts. > Hans > > > > > > > ------------------------------------------------------------------------------ > Achieve Improved Network Security with IP and DNS Reputation. > Defend against bad network traffic, including botnets, malware, > phishing sites, and compromised hosts - saving your company time, > money, and embarrassment. Learn More! > http://p.sf.net/sfu/hpdev2dev-nov > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > > ------------------------------------------------------------------------------ Achieve Improved Network Security with IP and DNS Reputation. Defend against bad network traffic, including botnets, malware, phishing sites, and compromised hosts - saving your company time, money, and embarrassment. Learn More! http://p.sf.net/sfu/hpdev2dev-nov _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
