Bugs item #3376708, was opened at 2011-07-24 19:47
Message generated for change (Tracker Item Submitted) made by mkjensen
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Category: Library Functions
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Martin Kamp Jensen (mkjensen)
Assigned to: Nobody/Anonymous (nobody)
Summary: OBMol.delete() crash in native code if containing conformers
Initial Comment:
If I load a PDB molecule and afterwards load an XTC trajectory for that
molecule (which seems to be the way to load a trajectory in Open Babel), then
at some point the JVM crashes due to a crash in native code. I found out the
reason is that the OBMol.finalize() method (which is called by the garbage
collector when there is no more references to an object) includes a call to
OBMol.delete() which is responsible for calling into the native code that then
crashes.
I have included the crash information in "crash.txt" and I will attach an
example molecule and trajectory later (I do not see the possibility for
multiple attachments). The code below is the reduced test case:
OBConversion conversion = new OBConversion();
conversion.SetInFormat("pdb");
OBMol molecule = new OBMol();
conversion.ReadFile(molecule, "/path/to/AcAANMe.pdb");
conversion.SetInFormat("xtc");
// Crash if next line is uncommented:
//conversion.ReadFile(molecule, "/path/to/trajectory.xtc");
molecule.delete();
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