OpenBabel error: conversion failed
when opening a .DAT output file from a GAMESS calculation (6,098 kB)
gamess.13-64.pgi.linux.blas.exe 64 bit windows version of GAMESS

I have been unable to load most output files for the calculations I am running. These are geometric optimizations of medium sized molecules (18 non-H atoms) via DFT

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: (1.90.0)
• Qt: (5.11.3)

Desktop version: (please complete the following information):

• OS: Debian GNU/Linux 10
• Version (of kernel: 4.19.0-13-amd64, if that is relevant)
• Compiler: GCC 8.3.0-6

Describe the bug
Could not compile the latest version because of a (copy/paste?) error in cmake/projects.cmake: line 36 was:

set(openbabel_version "openbabel-3-1-1")

instead of:

set(openbabel_version "3-1-1")

. When I make this correction, everything works well, and Avogadro is compiled (and runs flawlessly).

Now that translations are available, we should bundle them with the Mac and Windows builds and load them properly:
https://github.com/openchemistry/avogadro-i18n

The "Caffeine" label doesn't show up on my iPhone for some reason, so I can't tap it for more information.

Ideally, we'd bundle up a new Avogadro2 manual..

In the meantime, this was the menu in Avogadro 1.x:

• Manual
• FAQ
• Discussion Forum
• Report a Bug
• Website

Maybe a "credits?" .. Safari has "Acknowledgements" in the help menu.

In DetermineVersion.cmake, line 53:

if ("${major}.${minor}.${patch}" EQUAL "${full}")

shouldn't this be STREQUAL instead? VERSION_IS_RELEASE is always TRUE, i. e. when this is not the tag annotated release which is not the expected behaviour.

It would be very useful to be able to batch-generate inputs for Gaussian, when you have a multi-molecule file loaded, for example when you want to do conformational analysis.

One cannot drag-and-drop a file into the program window, and has to use the dialog File -> Open... to open it.

If I try to compile avogadro2 app with qt 5.8.0, I get this error:

avogadro/mainwindow.cpp: In function 'bool Avogadro::ToolSort(const Avogadro::QtGui::ToolPlugin*, const Avogadro::QtGui::ToolPlugin*)':
avogadro/mainwindow.cpp:1555:13: error: 'const class Avogadro::QtGui::ToolPlugin' has no member named 'priority'; did you mean 'property'?
return a->priority() < b->priority();
^~~~~~~~
avogadro/mainwindow.cpp:1555:29: error: 'const class Avogadro::QtGui::ToolPlugin' has no member named 'priority'; did you mean 'property'?
return a->priority() < b->priority();
^~~~~~~~

After reverting e509e77 the build is successful.

It looks like commit 98afc12 breaks the file menu, at least in my testing on Linux. I didn't really test this very much, but building things I get menus appearing where they shouldn't, broken recent file menu not showing recent files but showing export molecule/graphics. Moving to the commit before this and everything looks fine.

I am not sure I followed the logic looking through it again, and should have tested this more thoroughly before merging it. Any ideas on a fix, does this look normal on macOS @ghutchis?

Hi all.

• Avogadroapp version: 1.94.0 + system molequeue compiled from molequeue-0.9.0
• Avogadrolibs: 1.94.0 + bundled molequeue
• Qt: 5.15.2

Desktop version:

• OS: Fedora
• Version 34
• Compiler: GCC-11.1.1

Describe the bug

Additional question
avogadro2-libs-1.94.0 now provides molequeue in bundle; molequeue will be separately developed or will be always followed inside avogadro2-libs?

Hello,

GNOME and KDE will soon get their own software centers. There is a requirement for applications to ship an .appdata.xml file, which is to be placed in /usr/share/appdata, just like .desktop files are placed in /usr/share/applications. These files contain a description of each application, links to 16:9 screenshots and other information (e.g. homepage, project license etc.).

You can read about the specifics of AppData here:

people.freedesktop.org/~hughsient/appdata/
http://www.freedesktop.org/software/appstream/docs/chap-Quickstart.html

If you do not have the time, I would be more than happy to write one for you; I've been a long time Avogadro user and I would love to give something back. If you decide to prepare your own, please drop me a line, so that I may update the list of compatible applications in Fedora. I would also like to ask you to add that same file to the 1.x branch.

Best Regards

P.S.: I have sent the same message to kitware.com, but I was not sure if that was the appropriate route, so I am opening this issue.

This offers the fancier looking image, the Tomviz project is using it, can all be done in CPack/CMake.

In my work, I often need to view several 'molecules' (specified in XYZ file) from exactly same position. It would be nice to have a way to 'synchronize' the camera positions and view settings on all molecules. A possible simple and (I think) easy to implement enhancement to address this need would be a special box to copy/paste camera position/zoom in Avogadro

A more complex enhancement would be 'multiview' mode, that would open a set of molecules in tabs with camera position shared between all the tabs (and possibly with batch-open and batch-picture-export). This, however is not mutually exclusive with the previous option, ideally both should be implemented (but the first is more important, since it can be used instead of the second)

Hello,

I am trying the create Avogadro2 package for openSUSE Tumbleweed with openSUSE's Open Build Service (OBS).
OBS take source code and compile it using instructions inside .spec file.

This is the repository I am working on: https://build.opensuse.org/package/show/home:andythe_great/Avogadro2

The spec file include the following dependencies.

BuildRequires:  avogadrolibs-devel (1.93.0)
BuildRequires:  chrpath (0.16)
BuildRequires:  cmake (3.16.2)
BuildRequires:  desktop-file-utils (0.24)
BuildRequires:  doxygen (1.8.16)
BuildRequires:  eigen3-devel (3.3.7)
BuildRequires:  gcc-c++ (9-1.6)
BuildRequires:  glew-devel (2.1.0)
BuildRequires:  hdf5-devel (1.10.5)
BuildRequires:  hicolor-icon-theme (0.17)
BuildRequires:  libQt5OpenGL-devel (5.14.1)
BuildRequires:  libQt5OpenGL5 (5.14.1)
BuildRequires:  libqt5-qtbase-devel (5.14.1)
BuildRequires:  libqt5-qttools-devel (5.14.1)
BuildRequires:  libsymspg1 (1.14.1)
BuildRequires:  molequeue-devel (0.9.0)
BuildRequires:  python3-devel (3.7.3)
BuildRequires:  spglib-devel (1.14.1)
Requires:       openbabel3 (5463-1.1)
Requires:       python3 
Provides:       avogadroapp

This is the build flags inside the spec file.

%build
export CFLAGS="%{optflags} -I%{_includedir}/%{name}"
export CXXFLAGS="%{optflags} -I%{_includedir}/%{name}"
%cmake -Wno-dev \
 -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
 -DENABLE_RPATH:BOOL=ON \
 -DENABLE_TESTING:BOOL=OFF \
 -DAvogadroLibs_DIR:PATH=%{_libdir} \
 -DBUILD_DOCUMENTATION:BOOL=ON \
 -DCMAKE_BUILD_TYPE:STRING=Release \
 ..

This is the error I get

[    6s] -- Could NOT find Git (missing: GIT_EXECUTABLE) 
[    6s] -- Could not use git to determine source version, using version 1.93.0
[    6s] -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
[    6s] -- Found Doxygen: /usr/bin/doxygen (found version "1.8.16") found components: doxygen missing components: dot
[    6s] -- Configuring done
[    6s] CMake Error at avogadro/CMakeLists.txt:99 (add_executable):
[    6s]   Target "avogadro" links to target "Qt5::OpenGL" but the target was not
[    6s]   found.  Perhaps a find_package() call is missing for an IMPORTED target, or
[    6s]   an ALIAS target is missing?
[    6s] 
[    6s] 
[    6s] -- Generating done
[    6s] CMake Warning:
[    6s]   Manually-specified variables were not used by the project:
[    6s] 
[    6s]     BUILD_STATIC_LIBS
[    6s]     CMAKE_Fortran_FLAGS
[    6s]     CMAKE_INSTALL_DO_STRIP
[    6s]     CMAKE_MODULES_INSTALL_DIR
[    6s]     INCLUDE_INSTALL_DIR
[    6s]     LIB_INSTALL_DIR
[    6s]     LIB_SUFFIX
[    6s]     SHARE_INSTALL_PREFIX
[    6s]     SYSCONF_INSTALL_DIR
[    6s] 
[    6s] 
[    6s] CMake Generate step failed.  Build files cannot be regenerated correctly.
[    6s] error: Bad exit status from /var/tmp/rpm-tmp.C3Yy6I (%build)
[    6s] 
[    6s] 
[    6s] RPM build errors:
[    6s]     Bad exit status from /var/tmp/rpm-tmp.C3Yy6I (%build)

I believe that the cmake can't find Qt5OpenGL, but I'm not sure.

Thanks.

Avogadro version:

• Avogadro: 1.91.0
• Qt: 5.10.1

Desktop version:

• OS: Fedora
• Version: 28
• Compiler: 8.1.1

Describe the bug
Avogrado2 's window shows 1.90.0 as release number.

Expected behavior
1.91.0 release number

Screenshots

It is sometimes useful to be able to load a structure from a Gaussian input file. Also, being able to write but not read back Gaussian inputs is kinda confusing and annoying for new users.

Qt 5.10 changed the way that interface styles are packaged. In addition to the "platforms" plugin directory, there's also a "styles" directory.

If I compile with Qt 5.10+ on Mac, I normally see this:

If I copy the "styles" files "libqmacstyle.dylib" to the Plugins directory for deployment, everything looks okay:

I can tell that the DeployQt5.cmake files probably need revision, but I can't even tell where they're called or how to add in the updated files.

Any ideas @cryos ?
(I'd think many other apps have similar problems - most seem to directly use the windeployqt and macdeployqt programs instead.)

Dear Markus, Dear all,

i'm writing regarding this bug request. https://bugs.gentoo.org/649860

i realised that avogadroapp need the static library of jsoncpp which is required by avogadrolibs

Here the error code:

CMake Error at /usr/lib64/cmake/avogadrolibs/AvogadroLibsTargets.cmake:214 (message):
  The imported target "jsoncpp" references the file

     "/usr/lib64/libjsoncpp.a"

  but this file does not exist.  Possible reasons include:

  * The file was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and contained

     "/usr/lib64/cmake/avogadrolibs/AvogadroLibsTargets.cmake"

  but not all the files it references.

Call Stack (most recent call first):
  /usr/lib64/cmake/avogadrolibs/AvogadroLibsConfig.cmake:22 (include)
  avogadro/CMakeLists.txt:1 (find_package)

So, i wrote a jsoncpp revision ebuild to solve this problem. However the ebuild will not be accepted. https://bugs.gentoo.org/649860

How to fix this problem?
Is there any particular reason to use the static library instead of the dynamic one?

Thanks.
Best regards
GMR

Right now, there are two main JSON-RPC calls:

• openFile(filename)
• loadFile(data)

There's a definite need for other JSON-RPC calls to help with automation / scripting:

• saveFile(format) => bytestream or string
• saveFile(format, filename) => force a save
• renderImage(filename) => render current frame buffer
• renderAnimation(options) => step through coordinates to render the whole reaction / trajectory, etc.

I can imagine requesting particular rendering options would be useful

Some level of security analysis is needed (e.g., to make sure malformed request don't crash Avogadro, and to ensure RPC can be turned off as a preference even if compiled in).

Avogadro still needs python2 for its compilation even though it is not supported anymore. So, porting of avogadro to python3 should be done soon.

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: 1.93.0
• Qt: 5.14

Freshly pulled from git and compiled without errors trying to optimize geometry produces the stated error: "Error interpreting obabel MDL output".
It seems the way in which obabel is invoked is wrong.
OBProcess::executeObabel: Running "/home/usr/bin/openchemistry/prefix/bin/obabel" "-imol -omol --minimize --log --crit 1e-6 --ff GAFF --steps 2500 --rvdw 10 --rele 10 --freq 10" MDL: "Open Babel 2.4.1 -- Aug 14 2017 -- 14:41:50\nUsage:\nobabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]\nTry -H option for more information.\n"
the zlib linking issue in obabel (26) could also be the cause.

Needs translation options - both for Qt and for avogadrolibs

Dear developers,

could you provide flatpak support for avogadro2? I also made a rough preliminary sketch of the build manifest.

app-id: org.OpenChemistry.avogadro2
runtime: org.kde.Platform
runtime-version: "5.9"
sdk: org.kde.Sdk
command: flatpak-demo
finish-args: 
  - --share=ipc
  - --socket=x11
  - --socket=wayland
  - --filesystem=host
  - --device=dri
modules: 
- name: avogadro2
  buildsystem: cmake
  build-options:
    - build 
    - config 1.91.0 
  sources: 
    - type: git
      url: git://github.com/OpenChemistry/openchemistry

With that preliminary manifest I get as far as

...
-- Set runtime path of "/run/build/avogadro/prefix/bin/molequeue" to "/run/build/avogadro/prefix/lib"
[ 15%] Completed 'molequeue'
[ 15%] Built target molequeue
make: *** [Makefile:84: all] Error 2

but I don't know how the handle the error.

Regards

Hi,

On my i586 openSUSE Tumbleweed openSUSE Build Service (OBS) build target I get the cmake error:

[  135s] -- Detecting CXX compiler ABI info
[  136s] -- Detecting CXX compiler ABI info - done
[  136s] -- Detecting CXX compile features
[  139s] -- Detecting CXX compile features - done
[  139s] -- Performing Test HAVE_GCC_ERROR_RETURN_TYPE
[  139s] -- Performing Test HAVE_GCC_ERROR_RETURN_TYPE - Success
[  139s] -- Could NOT find Git (missing: GIT_EXECUTABLE) 
[  139s] -- Could not use git to determine source version, using version 1.90.0
[  139s] -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
[  139s] -- Found Doxygen: /usr/bin/doxygen (found version "1.8.14") found components:  doxygen missing components:  dot
[  139s] CMake Error at cmake/AvogadroCPack.cmake:37:
[  139s]   Parse error.  Expected "(", got newline with text "
[  139s] 
[  139s]   ".
[  139s] Call Stack (most recent call first):
[  139s]   CMakeLists.txt:73 (include)
[  139s] 
[  139s] 
[  139s] -- Configuring incomplete, errors occurred!
[  139s] See also "/home/abuild/rpmbuild/BUILD/avogadroapp-b1838d884908acfbcc2a1f61259e8bea78be811e/build/CMakeFiles/CMakeOutput.log".
[  139s] error: Bad exit status from /var/tmp/rpm-tmp.MluVGZ (%build)
[  139s] 

(ignore the [139s], it pertains to the build time in the OBS). The cmake command used is:

cmake -DCMAKE_BUILD_TYPE:STRING=Release \ 
 -Wno-dev \ 
 -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ 
 -DENABLE_RPATH:BOOL=ON \ 
 -DENABLE_TESTING:BOOL=OFF \ 
 -DAvogadroLibs_DIR:PATH=/usr/lib32 \ 
 -DBUILD_DOCUMENTATION:BOOL=ON .. 

This is an error I only have gotten with the latest git commit #407, b1838d8. Earlier commits built fine. Full log is here.

Thanks for your time and patience,
Brenton

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: (e.g. 1.90.0-316-g6d14770)
• Qt: (e.g., 5.9.5)

Desktop version: (please complete the following information):

• OS: Linux Mint 20.1
• Version 20.1
• Compiler gcc 9.3.0

Describe the bug
Context menu that appears when you right click on menubar has last two checkboxes unlabeled.

To Reproduce
Steps to reproduce the behavior:

1. Open Avogadro2.
2. Right click on menubar.
3. Context menu appears.
4. Last two checkboxes are unlabeled.

Expected behavior
Label the checkboxes.

Screenshots

Additional context
Add any other context about the problem here. Please consider uploading or linking test files.

I think we should merge the toolbars (like v1) which would greatly simplify highlighting one tool at a time. Since the code has merged, I think the user interface should simplify too.

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: (e.g. 1.90.0-316-g6d14770)
• Qt: (e.g., 5.9.5)

Desktop version: (please complete the following information):

• OS: [e.g. MacOS]
• Version [e.g. 10.12.4]
• Compiler (if you built from source)

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
If applicable, add screenshots to help explain your problem.

Additional context
Add any other context about the problem here. Please consider uploading or linking test files.

Hi,

I packaged the OpenChemistry packages needed to build this application from their respective latest master git commit, along with this application itself, using the openSUSE Build Service. Avogadro 2 launches fine, but there's an issue with running obabel in it to optimize geometry. I started Avogadro 2 from the command-line so I could see the precise error messages and commands it is executing, this is what I saw when trying to optimize the geometry of a molecule:

OBProcess::executeObabel: Running "obabel" "-imol -omol --minimize --log --crit 1e-6 --ff  --steps 10000 --rvdw 10 --rele 10 --freq 10"
MDL: "Open Babel 2.4.90 -- May 28 2018 -- 20:57\nUsage:\nobabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]\nTry  -H option for more information.\n"

seems like the command is not found. Open Babel must be working somewhat given that I managed to open a SDF file, which I think requires the Open Babel backend to work. I tried a few example Open Babel 3 commands, however, and they all returned errors. Like when I ran the example command:

obabel -:"O=C(O)c1ccccc1OC(=O)C aspirin" -:"Oc1ccccc1C(=O)O salicylic acid" -ofpt

(per the docs for 2.3.1, not sure if Open Babel 2 and 3 use the same syntax, however)

I received the output:

obabel: cannot write output format!
Open Babel 2.4.90 -- May 28 2018 -- 20:57
Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
Try  -H option for more information.

If you want to look at the files I used to build Open Babel 3, here they are. If you want to see the build log click the "Succeeded text" next to the "openSUSE Tumbleweed" build target on the right side bar. Here's a screenshot showing exactly what I mean for the Avogadro 2 libraries package:

. Avogadro 2 (i.e. avogadroapp) is here. The libraries (avogadrolibs) are here. MoleQueue is packaged here. spglib is here. I tried running an strace on the aspirin obabel command above, here is the output:

obabel.log

Here is strace output for opening a SDF file with Avogadro 2 and trying to optimize the geometry:

strace.log

I really want this Avogadro 2 build to work to its fullest potential so please, if there's something you need to know in order to help fix this ask.

Thanks for your time,
Brenton

Using Boost to replace C++11 smart pointers that are not available.
Boost version: 1.57.0
Adding cylinders_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/cylinders_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/cylinders_fs.h cylinders_fs
Adding cylinders_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/cylinders_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/cylinders_vs.h cylinders_vs
Adding linestrip_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/linestrip_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/linestrip_fs.h linestrip_fs
Adding linestrip_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/linestrip_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/linestrip_vs.h linestrip_vs
Adding mesh_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/mesh_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/mesh_fs.h mesh_fs
Adding mesh_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/mesh_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/mesh_vs.h mesh_vs
Adding spheres_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/spheres_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/spheres_fs.h spheres_fs
Adding spheres_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/spheres_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/spheres_vs.h spheres_vs
Adding sphere_ao_depth_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_depth_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_depth_vs.h sphere_ao_depth_vs
Adding sphere_ao_depth_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_depth_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_depth_fs.h sphere_ao_depth_fs
Adding sphere_ao_bake_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_bake_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_bake_vs.h sphere_ao_bake_vs
Adding sphere_ao_bake_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_bake_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_bake_fs.h sphere_ao_bake_fs
Adding sphere_ao_render_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_render_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_render_vs.h sphere_ao_render_vs
Adding sphere_ao_render_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_render_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/sphere_ao_render_fs.h sphere_ao_render_fs
Adding textlabelbase_fs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/textlabelbase_fs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/textlabelbase_fs.h textlabelbase_fs
Adding textlabelbase_vs.glsl to encoder... /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/textlabelbase_vs.glsl /home/henrique/Downloads/avogadrolibs-0.7.2/avogadro/rendering/textlabelbase_vs.h textlabelbase_vs
Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.6")
Using automoc for Qt library
Using automoc for Qt library
CMake Error at avogadro/qtplugins/CMakeLists.txt:98 (add_subdirectory):
add_subdirectory given source "bonding" which is not an existing directory.

CMake Warning (dev) at avogadro/qtplugins/crystal/CMakeLists.txt:28 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "CrystalScene". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/editor/CMakeLists.txt:24 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "Editor". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/manipulator/CMakeLists.txt:22 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "Manipulator". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/mongochem/CMakeLists.txt:14 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "MongoChem". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

Found Qt4: /usr/bin/qmake-qt4 (found version "4.8.6")
CMake Error at avogadro/qtplugins/CMakeLists.txt:115 (add_subdirectory):
add_subdirectory given source "playertool" which is not an existing
directory.

CMake Error at avogadro/qtplugins/CMakeLists.txt:116 (add_subdirectory):
add_subdirectory given source "povray" which is not an existing directory.

CMake Warning (dev) at avogadro/qtplugins/ballandstick/CMakeLists.txt:9 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "BallStick". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/vanderwaals/CMakeLists.txt:9 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "VanDerWaals". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at avogadro/qtplugins/CMakeLists.txt:129 (add_subdirectory):
add_subdirectory given source "wireframe" which is not an existing
directory.

CMake Warning (dev) at avogadro/qtplugins/meshes/CMakeLists.txt:9 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "Meshes". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/overlayaxes/CMakeLists.txt:18 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "OverlayAxes". All uses of target_link_libraries with a target
should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at avogadro/qtplugins/vanderwaalsao/CMakeLists.txt:9 (target_link_libraries):
Policy CMP0023 is not set: Plain and keyword target_link_libraries
signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy
details. Use the cmake_policy command to set the policy and suppress this
warning.

The keyword signature for target_link_libraries has already been used with
the target "VanDerWaalsAO". All uses of target_link_libraries with a
target should be either all-keyword or all-plain.

The uses of the keyword signature are here:

• avogadro/qtplugins/CMakeLists.txt:78 (target_link_libraries)

This warning is for project developers. Use -Wno-dev to suppress it.

Using automoc for Qt library
Configuring incomplete, errors occurred!
See also "/home/henrique/Downloads/avogadrolibs-0.7.2/CMakeFiles/CMakeOutput.log".
See also "/home/henrique/Downloads/avogadrolibs-0.7.2/CMakeFiles/CMakeError.log".

I am currently working on setting up a development environment for avogadroapp. I compiled the code on an up to date Arch Linux system, however I am running into:

1. A segmentation fault (specific keystrokes necessary)
2. General slow performance

For 1., I open the app, go to Draw mode, then attempt to draw an atom, and get a segmentation fault. I don't get the fault if I first open up a structure, then go to Draw, and attempt to draw an atom. I ran gdb to back-trace the segmentation fault. The relevant output:

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6c25730 in Avogadro::QtGui::RWMolecule::addAtom (this=0x0, num=6 '\006') at /home/barrymoo/src/openchemistry/avogadrolibs/avogadro/qtgui/rwmolecule.cpp:119
119   Index atomId = static_cast(m_molecule.m_atomicNumbers.size());
(gdb) bt
#0  0x00007ffff6c25730 in Avogadro::QtGui::RWMolecule::addAtom (this=0x0, num=6 '\006') at /home/barrymoo/src/openchemistry/avogadrolibs/avogadro/qtgui/rwmolecule.cpp:119
#1  0x00007ffff78a612d in Avogadro::QtPlugins::Editor::emptyLeftClick (this=0xa0eb20, e=0x7fffffffda20)
    at /home/barrymoo/src/openchemistry/avogadrolibs/avogadro/qtplugins/editor/editor.cpp:236
#2  0x00007ffff78a59c2 in Avogadro::QtPlugins::Editor::mousePressEvent (this=0xa0eb20, e=0x7fffffffda20)
    at /home/barrymoo/src/openchemistry/avogadrolibs/avogadro/qtplugins/editor/editor.cpp:103
#3  0x00007ffff7bd3127 in Avogadro::QtOpenGL::GLWidget::mousePressEvent (this=0x7173f0, e=0x7fffffffda20)
    at /home/barrymoo/src/openchemistry/avogadrolibs/avogadro/qtopengl/glwidget.cpp:267
#4  0x00007ffff567a4bf in QWidget::event(QEvent*) () from /usr/lib/libQt5Widgets.so.5
#5  0x00007ffff5636acc in QApplicationPrivate::notify_helper(QObject*, QEvent*) () from /usr/lib/libQt5Widgets.so.5
#6  0x00007ffff563c7d3 in QApplication::notify(QObject*, QEvent*) () from /usr/lib/libQt5Widgets.so.5
#7  0x00007ffff4d50dbb in QCoreApplication::notifyInternal(QObject*, QEvent*) () from /usr/lib/libQt5Core.so.5
#8  0x00007ffff563b2ea in QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool) ()
   from /usr/lib/libQt5Widgets.so.5
#9  0x00007ffff56924d0 in ?? () from /usr/lib/libQt5Widgets.so.5
#10 0x00007ffff5694643 in ?? () from /usr/lib/libQt5Widgets.so.5
#11 0x00007ffff5636acc in QApplicationPrivate::notify_helper(QObject*, QEvent*) () from /usr/lib/libQt5Widgets.so.5
#12 0x00007ffff563bf10 in QApplication::notify(QObject*, QEvent*) () from /usr/lib/libQt5Widgets.so.5
#13 0x00007ffff4d50dbb in QCoreApplication::notifyInternal(QObject*, QEvent*) () from /usr/lib/libQt5Core.so.5
#14 0x00007ffff507e752 in QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) () from /usr/lib/libQt5Gui.so.5
#15 0x00007ffff5080305 in QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*) () from /usr/lib/libQt5Gui.so.5
#16 0x00007ffff50651ef in QWindowSystemInterface::sendWindowSystemEvents(QFlags) () from /usr/lib/libQt5Gui.so.5
#17 0x00007fffe25d41b0 in ?? () from /usr/lib/qt/plugins/platforms/libqxcb.so
#18 0x00007fffe97d49fd in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0
#19 0x00007fffe97d4ce0 in ?? () from /usr/lib/libglib-2.0.so.0
#20 0x00007fffe97d4d8c in g_main_context_iteration () from /usr/lib/libglib-2.0.so.0
#21 0x00007ffff4da91b7 in QEventDispatcherGlib::processEvents(QFlags) () from /usr/lib/libQt5Core.so.5
#22 0x00007ffff4d4e852 in QEventLoop::exec(QFlags) () from /usr/lib/libQt5Core.so.5
#23 0x00007ffff4d5622c in QCoreApplication::exec() () from /usr/lib/libQt5Core.so.5
#24 0x00000000004277d8 in main (argc=1, argv=0x7fffffffe4f8) at /home/barrymoo/src/openchemistry/avogadroapp/avogadro/avogadro.cpp:99

With the help of some colleagues, I can reproduce the segmentation fault on Ubuntu (but not Fedora). Unfortunately, I don't know where to go from here.

For 2., On Arch Linux and Fedora, when drawing atoms, the performance is quite poor (on Ubuntu the GLWidget, which I believe is the name for the display, won't appear and I don't know the performance). It can take a few seconds to press and drag an atom across the screen (A different Fedora machine with a 1GB dedicated graphics card runs more smoothly). It may be that 1. and 2. are related, however the former problem causes a segmentation fault. It may just be the system specs are too poor to adequately use Draw mode, but freely rotating a molecule in "Navigate" works flawlessly. Note, that I have installed the pre-built package on my Windows 8 machine and the program runs flawlessly. All of the packages have been installed using the package managers from the Linux distribution (pacman, yum, and apt-get. I built against the downloaded version of Qt 5.4 from the website with the same segmentation fault (the only change is the location of libQt5Widget.so). I would gladly supply additional information and would help testing the software. Thank you.

Hi,

It'd be great if there was a "Preferences" item in the "Edit" menu that would launch a popup wherein you could edit, among other things, keyboard shortcuts used by Avogadro 2. Like I'd like to set Ctrl+Shift+A as the shortcut for "Save As".

The option to set a custom colour palette for the elements (e.g. black for carbon would be one I'd set pretty quickly) and background in a Preferences popup would also be helpful. Like the palette would have a set of defaults that come with the program (e.g. the grey for carbon, white for hydrogen, blue for nitrogen, etc. that Avogadro 2 uses by default), but you, the user, could customize the colour of each element to match your own preferences.

It'd be lovely if these preferences (shortcuts + colour + w/e else you's decide to add to it) could be saved so that when you open Avogadro 2 later you don't have to fiddle with them again, although a "Return to defaults" option would also be handy (which would reset the palette to the defaults the Avogadro 2 program came with).

I know in Avogadro 1, at least, you could set element colour but I think it is overly complicated having to fiddle with selections and display types options to change element colours when it could be simplified by a colour palette in a Preferences popup. This is a feature I know that Accelrys Discovery Studio Visualizer has and I, for one, quite like it.

Thanks for your time and patience,
Brenton

Is it possible to provide a Linux build of Avogadro2 along with the Windows and macOS builds? Perhaps in the form of a .deb package?

The web components introduce a perceived runtime dependency on BluetoothApis.dll, which cannot be resolved, and breaks packaging for the Windows platform. This looks like an issue with the Qt5 web component DLLs, but will need further investigation. Short term it may be necessary to disable any plugins requiring the web components.

Hi, I'm trying to install OpenChemistry on RHEL 8.0, basically because I want Avogadro2. I'm following the installation instructions from the openchemistry_build. However, close to the end of the installation, it stops with the message below. Would you be able to tell me what I'm missing?

Thanks a lot!

$ cmake --build . --config Release
[...]
[ 97%] Building C object tar/CMakeFiles/bsdtar.dir/__/libarchive_fe/passphrase.c.o
[ 98%] Linking C executable ../bin/bsdtar
../libarchive/libarchive.a(archive_read_support_format_rar5.c.o): In function `reset_file_context':
/home/seabra/work/source/repos/openchemistry/openchemistry-build/thirdparty/libarchive-src/libarchive/archive_read_support_format_rar5.c:853: undefined reference to `blake2sp_init'
../libarchive/libarchive.a(archive_read_support_format_rar5.c.o): In function `update_crc':
/home/seabra/work/source/repos/openchemistry/openchemistry-build/thirdparty/libarchive-src/libarchive/archive_read_support_format_rar5.c:2353: undefined reference to `blake2sp_update'
../libarchive/libarchive.a(archive_read_support_format_rar5.c.o): In function `verify_checksums':
/home/seabra/work/source/repos/openchemistry/openchemistry-build/thirdparty/libarchive-src/libarchive/archive_read_support_format_rar5.c:3870: undefined reference to `blake2sp_final'
collect2: error: ld returned 1 exit status
gmake[5]: *** [tar/CMakeFiles/bsdtar.dir/build.make:224: bin/bsdtar] Error 1
gmake[4]: *** [CMakeFiles/Makefile2:1173: tar/CMakeFiles/bsdtar.dir/all] Error 2
gmake[3]: *** [Makefile:141: all] Error 2
gmake[2]: *** [thirdparty/CMakeFiles/libarchive.dir/build.make:114: thirdparty/libarchive-prefix/src/libarchive-stamp/libarchive-build] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:367: thirdparty/CMakeFiles/libarchive.dir/all] Error 2
gmake: *** [Makefile:84: all] Error 2

Avogadro version:
Installed from "yum install", on a Linux cluster running CentOS 7:

• Avogadrolibs: avogadro2-libs.x86_64 0:1.90.0-12.el7
• Qt: qt.x86_64 1:4.8.7-3.el7_6

Desktop version:
Desktop machine is the graphics client, displaying windows:

• OS: Mac OS X 10.12.16
• XQuartz 2.7.11
• Late 2011 MacBook Pro, with stock graphics card (Intel HD Graphics 3000)

Describe the bug

Window that displays molecules is messed up, with pieces of other desktop windows randomly scattered inside.

To Reproduce

Window is immediately messed up on launch, rather than black.

Screenshots

It would be great if Avogadro could, after opening an XYZ file with multiple geometries, use the energy embedded in the comment line to create an energy plot. (X axis for the geometry number, Y axis for energy)
Here is a mock-up of an XYZ file that should be handled:
2
MP2/cc-pVTZ Energy: -2.0000000
C 0.0 0.0 0.0
O 1.0 1.0 1.0
2
DFT Energy: -1.5
C 0.00 0.000 0.00000
O 1.000 1.0 1.0050
2
-1.005
C 0.00 0.000 0.00000
O 1.000 1.0 2.0050

This should cover most of the variation that is commonly encountered.

Avogadro2 crashes when I attempt to measure more than two atoms. The first two atoms can be selected and the distance between them appears; however, upon selecting the third atom the program crashes with the following output:

SymmetryScene::process
Missing origo or radius
SymmetryScene::process
Missing origo or radius
SymmetryScene::process
Missing origo or radius
zsh: segmentation fault (core dumped)  ./avogadro2 ~/tmp/orca/IrCl6/geom.xyz

This happens no matter what atoms I try to measure: on symmetric and asymmetric molecules, when I load a file from the command line as while as within the app using open, and when I measure bonded or non-bonded distances.

Here is the full output I get when running avogadro:

Extension plugins dynamically found... 24
OBProcess::executeObabel: Running "obabel" "-L formats read"
OBProcess::executeObabel: Running "obabel" "-L formats write"
OBProcess::executeObabel: Running "obabel" "-L forcefields"
OBProcess::executeObabel: Running "obabel" "-V"
"obabel"  found:  "obabel: Open Babel 2.3.2 -- Oct 24 2016 -- 09:36:56"
Checking for generator scripts in "/home/vandezande/.local/share/OpenChemistry/Avogadro/scripts/workflows"
Checking for generator scripts in "/usr/share/ubuntu/OpenChemistry/Avogadro/scripts/workflows"
Checking for generator scripts in "/usr/local/share/OpenChemistry/Avogadro/scripts/workflows"
Checking for generator scripts in "/usr/share/OpenChemistry/Avogadro/scripts/workflows"
Checking for generator scripts in "/var/lib/snapd/desktop/OpenChemistry/Avogadro/scripts/workflows"
Checking for generator scripts in "/home/vandezande/progs/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/workflows"
Checking for generator scripts in "/home/vandezande/progs/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/inputGenerators"
Checking for file format scripts in "/home/vandezande/progs/openchemistry-build/avogadroapp/bin/../lib/avogadro2/scripts/formatScripts"
SymmetryScene constructor
SymmetryScene::process
Missing origo or radius
"Navigator" added
"Editor" added
"Selection" added
"Manipulator" added
"BondCentric" added
"MeasureTool" added
"PlayerTool" added
SymmetryScene::process
Missing origo or radius
SymmetryScene::process
Missing origo or radius
SymmetryScene::process
Missing origo or radius
SymmetryScene::process
Missing origo or radius
zsh: segmentation fault (core dumped)  ~/progs/openchemistry-build/avogadroapp/bin/avogadro2 geom.xyz

When using high-resolution "retina" mode on the Mac, draw / measure, etc. are unreliable, probably because of the conversion from display pixels.

I suspect this needs conversion via:
widget->windowHandle()->devicePixelRatio()
http://blog.qt.digia.com/blog/2013/04/25/retina-display-support-for-mac-os-ios-and-x11/

This is a feature that works well in Avogadro 1, but it is currently bugged in A2, only one of the molecules is loaded.

There should be a central settings dialog:

• Set the python path
• Add paths for fragments, scripts, etc.
• Add fog, depth-effects, etc.?
• Set translation

As far as I can tell, there's only an app icon, but nothing for document types (e.g., CML, CJSON, etc.).

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: 1.93.0
• Qt: 5.12.8

Desktop version: (please complete the following information):

• OS: Ubuntu LTS
• Version 20.04
• Compiler - precompiled and installed through Ubuntu Software tool

Describe the bug

Trying to install plugins. They appear to download using the 'Plugin Downloader". I can see the folder
~/.local/share/OpenChemistry/Avogadro/ has 'inputGenerators' with the folder
'OpenChemistry-avogenerators-4672519' which contains the *.py files. However, the inputgenerator does not appear in the Extension or Quantum menus.

The same behavior is observed for all the plugins. They can be downloaded but the application does not recognize they were downloaded.

Thanks,

Jape

To Reproduce
Steps to reproduce the behavior:

1. Go to 'Extensions'
2. Click on '.Plugin Downloader'
3. Select an update
4. go to '~/.local/Avogadro' directory see plugin directory created, but plugins do not work.

Expected behavior
Plugins to install after downloaded.

Avogadro version: (please complete the following information from the About box):

• avogadro2-libs-1.90.0-12
• Qt: 5.9.2

Desktop version: (please complete the following information):

• OS: Linux Scienfitic Linux (compatible with Redhat EL7)
• Version: 7.6
• Compiler: gcc-c++-4.8.5-39.el7.x86_64, cmake-2.8.12.2-2.el7.x86_64

Describe the bug
"File" -> "Import" on the desktop application shows only "Download by Name". On Mac, it has "Fetch from PDB", "Molecular file" etc.
"Build" menu on the desktop application does not show at all.

To Reproduce
Steps to reproduce the behavior:

1. Open Avogadro2 desktop application

2. Click on 'File' --> 'Import'

3. See the list

4. No "build" menu.

Expected behavior
I expect the menu of "import" and "build"

Additional context
I used the official builds of Avogadro2 version 1.90 packages in Redhat EL7. I built also them from source files on my computer. But, the proper menu does not come up. Is there any way to put the menu like Mac? Do we need version 1.93?

I'm writing PKGBUILDs for the different OpenChemistry components (MongoChem is still a WIP):

• molequeue: https://aur4.archlinux.org/molequeue-git.git/
• avogadrolibs: https://aur4.archlinux.org/avogadrolibs-git.git/
• avogadroapp: https://aur4.archlinux.org/avogadro2-git.git/

There aren't any issues during compilation, but it segfaults immediately. GDB reveals:

(gdb) backtrace 
#0  0x00007fffe764fc34 in ?? () from /usr/lib/libQtGui.so.4
#1  0x00007ffff7dea0ea in call_init.part () from /lib64/ld-linux-x86-64.so.2
#2  0x00007ffff7dea1fb in _dl_init () from /lib64/ld-linux-x86-64.so.2
#3  0x00007ffff7ddbdba in _dl_start_user () from /lib64/ld-linux-x86-64.so.2
#4  0x0000000000000001 in ?? ()
#5  0x00007fffffffe42a in ?? ()
#6  0x0000000000000000 in ?? ()

It looks like both Qt4 and Qt5 versions of the same library are getting linked in:

[eric@osmium]$ ldd avogadro2 | grep -i "qt"
2:  libAvogadroQtOpenGL.so => /usr/lib/libAvogadroQtOpenGL.so (0x00007f7b796a4000)
3:  libAvogadroQtPlugins.so => /usr/lib/libAvogadroQtPlugins.so (0x00007f7b79371000)
7:  libQt5OpenGL.so.5 => /usr/lib/libQt5OpenGL.so.5 (0x00007f7b78ad9000)
8:  libAvogadroQtGui.so => /usr/lib/libAvogadroQtGui.so (0x00007f7b7886a000)
9:  libQt5Widgets.so.5 => /usr/lib/libQt5Widgets.so.5 (0x00007f7b77fb6000)
10: libQt5Gui.so.5 => /usr/lib/libQt5Gui.so.5 (0x00007f7b7784a000)
11: libQt5Core.so.5 => /usr/lib/libQt5Core.so.5 (0x00007f7b7715d000)
15: libQtNetwork.so.4 => /usr/lib/libQtNetwork.so.4 (0x00007f7b766fd000)
23: libQt5Concurrent.so.5 => /usr/lib/libQt5Concurrent.so.5 (0x00007f7b749a8000)
26: libQt5Network.so.5 => /usr/lib/libQt5Network.so.5 (0x00007f7b741de000)
28: libvtkGUISupportQtOpenGL-6.1.so.1 => /usr/lib/libvtkGUISupportQtOpenGL-6.1.so.1 (0x00007f7b73c97000)
56: libQtCore.so.4 => /usr/lib/libQtCore.so.4 (0x00007f7b6e438000)
67: libvtkGUISupportQt-6.1.so.1 => /usr/lib/libvtkGUISupportQt-6.1.so.1 (0x00007f7b69f72000)
68: libQtOpenGL.so.4 => /usr/lib/libQtOpenGL.so.4 (0x00007f7b69c6e000)
69: libQtGui.so.4 => /usr/lib/libQtGui.so.4 (0x00007f7b68f35000)

The GitHub actions should build an AppImage using linuxdeploy on 18.04 (for now)

The related avogadrolibs action is:
OpenChemistry/avogadrolibs#561

Steps to reproduce:

1. Launch the program and select any background color
2. Close and launch again
3. Observe that background is black

When launched, the default (of course) is to activate the draw tool. But the icon is not highlighted in the toolbar.

Current behavior is difficult, and unintuitive, it needs to be improved.