Avogadro 1.97.0

Avogadro 1.97 Release Notes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many 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

You can download Linux, Windows, and Mac versions at: https://github.com/openchemistry/avogadrolibs/releases/latest

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.

Highlights (tldr)

• Adds molecular surfaces, solvent-accessible, and solvent-excluded surfaces
• Adds support for a range of partial charge models, including coloring electrostatic potentials on surfaces.
  • This includes writing Python scripts to assign atomic charges or electrostatic potential
• Adds improved hydrogen-bond, chalcogen, and halogen bond rendering.
• Add improved close-contact and salt-bridge rendering
• Significantly improves interface translation, properly loading translation files, and including a dialog to choose your preferred user interface language (thanks to @ovari for significant help)
  • Includes English, Hungarian, Serbian, Esperanto, Portuguese, Turkish, German, Georgian, French, and Japanese translations with at least 45% coverage. Anyone can help via Weblate
• Now supports VTK-9 and Mac and Windows packages are updated to use Qt 5.15.

✨ Features

• Add tabbed interface to Close Contacts plugin @aerkiaga (#1026)
• Add "select backbone" and "select sidechain" commands @ghutchis (#1023)
• Initial salt bridge rendering @aerkiaga (#1021)
• Implement support for Turbomole coord format (also used by xtb) @ghutchis (#1012)
• Add ability to choose charge model in Surfaces @aerkiaga (#1016)
• Color electrostatic mesh @aerkiaga (#997)
• Add select water, enlarge selection and shrink selection @ghutchis (#1011)
• Enable editing of atom, bond, angle, torsion properties @ghutchis (#913)
• Add AM1-BCC charges using antechamber @ghutchis (#999)
• Add Python charge scripts. First example xtb GFN2 charges @ghutchis (#998)
• Enable Open Babel charge models, including caching partial charges @ghutchis (#984)
• Add arrow key navigation of the periodic table @ghutchis (#982)
• Assign atom colors by partial charges @ghutchis (#986)
• Implement basic tabbed interface for NonCovalent rendering @aerkiaga (#969)
• Implement basic hydrogen bond rendering @aerkiaga (#926)
• Add "Automatic" resolution, smoothing pass UI, optimization @aerkiaga (#976)
• Implement Laplacian mesh smoothing @aerkiaga (#975)
• Implement Solvent Excluded Surfaces @aerkiaga (#972)
• Initial electrostatics framework @ghutchis (#970)
• Add molecular surfaces code @aerkiaga (#897)
• Add missing acceptors and make distance relative (non-covalent) @aerkiaga (#966)
• Add halogen and chalcogen bonds, tune parameters @aerkiaga (#949)
• Add electron pair angle check for hydrogen bonds @aerkiaga (#946)
• Add line widths to the non-covalent / h-bond rendering @ghutchis (#934)
• Make use of angle tolerance for hole detection @aerkiaga (#939)
• Rename intensities to IR and add Raman intensities if available @ghutchis (#938)
• Check for Open Babel CJSON support: use it if available @ghutchis (#937)

🐛 Bug Fixes

• Clarify error messages of chargeScripts when antechamber or xtb is unavailable @e-kwsm (#1039)
• Fix input generators (and other scripts) with translation @ghutchis (#1037)
• Fix crash when layer names are translated (hu_HU right now) @ghutchis (#1038)
• Fix two minor input generator bugs @ghutchis (#1033)
• Drop alpha channel in the OpenGL context on Linux to avoid transparent windows
• Fix crashes in Surfaces and Select Backbone @aerkiaga (#1031)
• Workaround charge models locking up or not running @aerkiaga (#1020)
• Make sure to process events while rendering an animation @ghutchis (#1030)
• No longer bundle the "scale" example script - these can be downloaded @ghutchis (#1029)
• Use single-point calculation for AM1-BCC with Antechamber @ghutchis (#1002)
• When finding connected atoms, only ignore rings containing the bond @ghutchis (#1006)
• Fix incorrect hydrogen geometries @aerkiaga (#980)
• GAMESS-US and NWChem output reader sanity check @TiborGY (#930)
• Add case-insensitive lookup for file extensions @ghutchis (#935)

🚀 Performance Improvements

• Optimize mesh smoothing @aerkiaga (#985)

🧰 Maintenance

• Allow more render plugins to be "layer enabled" @ghutchis (#1008)
• Modernize using clang tidy fixes @ghutchis (#1005)
• Use float within Cube instead of double @aerkiaga (#990)
• Switch to a new clang-tidy script for secure pull-request comments @ghutchis (#988)
• Fix notarization for Mac M1 builds @ghutchis (#981)
• Bump Qt version to 5.15.2 (LTS) now that VTK-9 is working @ghutchis (#977)
• Port vtk9 @cryos (#973)
• Update source header comments to new format @ghutchis (#965)
• Fix some inconsistent overrides and headers @ghutchis (#960)
• Build Mac M1 binaries on self-hosted runner @ghutchis (#936)
• Fix error when notarizing Mac DMG - use the right working dir @ghutchis (#927)

📚 Translations

• Fix bug to successfully load translation files
• Automated translation updates
• Fix translation errors with About menu item and 3D View button @ghutchis
• Make sure to install qt base translations for Mac and Windows @ghutchis
• Make sure that render names in the layer list show up w/ i18n @ghutchis (#992)
• Translate editor element list @ghutchis (#964)
• Fix several i18n problems @ghutchis (#956)
• Make sure to translate menu paths for Python scripts. @ghutchis (#948)
• Translations update from Hosted Weblate @weblate (#928)

Credits

Thanks to many contributors, including: @NorwayFun, @TiborGY, @aerkiaga, @ahenao, @artemmolotov, @cryos, @e-kwsm, @ghutchis, @github-actions, @matterhorn103, @ovari, @tacitcoast, @usta, @weblate, Julen Larrucea, Translator and МАН69К