Bugs item #3058701, was opened at 2010-09-03 11:39 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3058701&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Translation Group: 2.3.x Status: Open Resolution: None Priority: 7 Private: No Submitted By: Noel O'Boyle (baoilleach) Assigned to: Noel O'Boyle (baoilleach) Summary: Segfault SMILES parsing of stereo at S Initial Comment: >From Peter Lavin via private email: I am using the following SMILES file from ZINC... http://zinc.docking.org/subset1/13/13_t80.smi I am getting segmentation faults when I attempt to convert all 149K of these SMILES strings using the following command... babel --gen3d -ismi 13_t80.smi -osdf myOutFile.sdf I have narrowed the problem down to a pattern which appears in some molecules. The problem pattern appears to be S@ and this appears for example in line 89, 565, 906, 1031, 1049, 1050, 1165, 1175, 1176, 1266, etc. Interestingly, the string at line 1049 converts ok (pasted here) c...@](=N)(=O)c1ccccc1 ZINC12402895 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3058701&group_id=40728 ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
