Avogadro 1.96.0#

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

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