Bugs item #3568884, was opened at 2012-09-18 04:53 Message generated for change (Tracker Item Submitted) made by joannakocot You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3568884&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: Library Functions Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Joanna (joannakocot) Assigned to: Nobody/Anonymous (nobody) Summary: Segmentation fault when converting with java bindings Initial Comment: A segmentation fault appears when calling OBConversion.Read() from OpenBabel java API on a specific xyz file. The file is available here: http://virolab.cyfronet.pl/~asia/e3-dprot.xyz (I didn't manage to submit it here - maybe because it's quite large). The code below works fine for other files, but for this one I get a segmentation fault when Read() is called. OBMol mol = new OBMol(); OBConversion c = new OBConversion(); c.SetInFormat("xyz"); c.SetOutFormat("pdb"); // same with c.SetOutFormat("xyz"); boolean readResult = c.ReadFile(mol, filePath); The same file is properly converted if command-line openbabel is used (however I managed to observe an infinite loop once, but didn't manage to reporoduce it later). Appeared on version 2.3.1 with java 1.7.0_05 on Scientific Linux 5 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3568884&group_id=40728 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
