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Segfaults on creating 3d geometry


#1

The RInChI source code has some test .mol files. When I view them in Avogadro 1.2.0,
there is a dialog asking if I want it to build a 3D geometry. If I select “no”, all is fine, and I
see a flat molecule. If I select “yes” there is a segfault.

"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: "
Locale: "en_US"
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
Loading plugins: "/usr/bin/…/lib64/avogadro/1_2"
Searching for plugins in "/usr/lib64/avogadro/1_2"
Searching for plugins in "/usr/lib64/avogadro/1_2/colors"
Searching for plugins in "/usr/lib64/avogadro/1_2/engines"
Searching for plugins in "/usr/lib64/avogadro/1_2/extensions"
Searching for plugins in "/usr/lib64/avogadro/1_2/tools"
Loading plugins: "/root/.avogadro/1_2/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x24e9f30 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
Could not find python module…
dev warning: Extension “Python Terminal” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
HOMO at: -1
GLWidget initialisation…
GLWidget initialised…
read 1 molecules.
createObjects()
Segmentation fault

Built from souce on GNU/Linux 64-bit with GCC 7.3.0 and glibc 2.26.


#2

Do you think you can point me at the file in question? In this case, the bug would be in Open Babel - it should be fixed in the current OB code, since that reads RInChI, but I’d like to verify.

Thanks!


#3

1.00\ RInChI/rinchi/test/V3000_molfiles/Elements_C2m1_V3000.mol
for example, from RInChI-V1-00.zip

But it’s a mol file, not an rxn.

And obgui didn’t choke on it.