Avogadro v1.96.0#
2 June 2022
Changes#
We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements, including contributions from @aerkiaga as part of Google Summer of Code. Thanks to many for suggestions, bug reports, and discussions.
Draft developer documentation can be found at https://two.avogadro.cc
As part of this release, we have an official AppImage build for Linux, as well as a code-signed release for macOS.
If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions in many forms are very welcome, particularly if you’d like to help with user documentation or website developement.
✨ Features#
Insert DNA/RNA dialog @ghutchis (#909)
Render close contacts @aerkiaga (#898)
Create new layer from selection @ghutchis (#899)
Tweak the mesh lighting … now lights “from the top” @ghutchis (#880)
Add an initial config widget to set mesh colors and opacity @ghutchis (#877)
Import and retain space group information @ghutchis (#875)
Write Gaussian cube files @ghutchis (#873)
Add plugin to focus or unfocus selection @aerkiaga (#868)
Implement close contact perception logic @aerkiaga (#862)
Add formal charge to atom property tables @ghutchis (#839)
Add support for formal charges @aerkiaga (#831)
Add setting to reverse direction of scroll-to-zoom @ghutchis (#778)
Tweak icons for label editor and selection @ghutchis (#776)
Add tooltips to tools @ghutchis (#777)
Add label editor to create custom labels @serk12 (#740)
Add a copy graphics action
🚀 Performance Fixes#
Subgraph rewrite @aerkiaga (#878)
Approximate cartoon B-spline from a small local neighborhood @aerkiaga (#860)
Bond graph optimization @aerkiaga (#832)
Faster bond perception @aerkiaga (#829)
Optimize secondary structure @aerkiaga (#833)
🐛 Bug Fixes#
Add .cjson extension to files if none is present
Update atomic masses @ghutchis (#894)
Fix layer memory crash @ghutchis (#876)
Fix memory leak with OpenGL: Detaching and deleting shaders/programs on updates @octycs (#855)
Remove call for Core::Molecule rendering to eliminate casting @ghutchis (#871)
Fix reading generic file formats with Open Babel @ghutchis (#848)
Fix erratic editing behavior @aerkiaga (#819)
Solve problems writing files with no extension @ghutchis (#835)
Convert 2-letter PDB symbols to appropriate case @aerkiaga (#830)
Fix Manipulation and Bond Centric Manipulation tools @aerkiaga (#825)
Fall back to Wikipedia method for dihedral angles @ghutchis (#808)
Be careful about assign or copy from molecules with no layers @ghutchis (#806)
Disable dynamic bonding during animation @ghutchis (#767)
Try to use ‘python’ in the path as a fallback @ghutchis (#746)
🧰 Maintenance#
Fix Valgrind uninitialized errors @aerkiaga (#887)
Add tests using various sanitizers @ghutchis (#888)
Make sure to sign and notarize the Mac build @ghutchis (#893) (#885)
Only build overlayaxes if USE_OPENGL is enabled @ghutchis (#879)
Try using Windows 2019 to build wheels @ghutchis (#861)
Create Codacy scans @ghutchis (#850)
test “>=0” within machine precision (>-EPS) @drew-parsons (#813)
Add defaultBehavior method to render plugins @serk12 (#807)
Update setup.py with long description from README.md and URLs @ghutchis (#750)
📚 Translations#
Translations update from Hosted Weblate @weblate
Automated translation updates @github-actions (#853)
Minor tweaks to the automated pull request @ghutchis (#761)
Credits#
Thanks to many contributors, including: @HoangTuan110, @Lisapple, @M3CG, @SantosSi, @aerkiaga, @comradekingu, @drew-parsons, @ejatjon, @ersen0, @ghutchis, @github-actions, @github-actions[bot], @milotype, @nicolasfella, @octycs, @ovari, @rezaalmanda, @serk12, @urkawa, @weblate, J. Lavoie, Pa, Temuri Doghonadze, phlostically and 刘韬