OpenChemistry/avogadrolibs 1.97.0

Avogadro 1.97.0

on GitHub

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