Avogadro 1.97.0#

21 July 2022

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: openchemistry/avogadrolibs

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

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