Avogadro 1.97 Release

Announcements
1

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: Release Avogadro 1.97.0 · OpenChemistry/avogadrolibs · GitHub

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.

:sparkles: 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: 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)

:rocket: Performance Improvements

:toolbox: 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)

:books: 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