Avogadro 1.100.0

🌟 Highlights (tldr)

• New rendering options, including depth-of-field blur and fog from @perminder-17
• Faster surface mesh generation using the flying edges algorithm @perminder-17
• Brought back the "molecular orbitals" panel @ghutchis
• Support for translucent balls-and-sticks, van der Waals spheres, and licorice rendering including per-layer customization @ghutchis
• New, improved Flatpak package from @matterhorn103 including support for ARM
• New conformer properties window @ghutchis
• New improved molecular properties window, including charge and spin multiplicity, HOMO and LUMO energies, total energies and other properties (depending on file format) @ghutchis
• Many more properties parsed from ORCA output files including Hirshfeld, MBIS, and CHELPG charges @ghutchis
• Code signing on Windows to minimize Defender warnings @ghutchis thanks to SignPath
• Support for latest Qt6 on Linux @matterhorn103

✨ Features

• Improved spectra plots, including NMR, UV and CD spectra
• Add support for reading and rendering DNA / RNA backbones
• Improve python selection dialog
• Calculate and render dipole moments
• Edit molecule name, charge, and spin in properties
• Improve manipulate dialog - rotate around origin, molecule center, selection center
• Update the template tool to place ligands or functional groups
• Support for additional secondary structures (3-10 and pi helix) @TactfulDeity
• Implement g orbitals
• cp2kinput improvements @e-kwsm
• Add support to render atomic partial charge labels
• Add support to render bond lengths
• Add HOMO and LUMO energies to molecular properties
• Add Shortcut Keys to navigate/modify tools (Issue #1794) @Milziade
• Add "change elements" dialog
• Editing molecular charge / spin => input generators and plugins

📄 File Format Improvements:

• Parse inputParameters if present in cjson
• Read radicals from SDF / Molfile
• Parse more MOPAC aux properties including coordinates
• Parse CHELPG charges from ORCA output too
• Export to XYZ format with 10 decimal precision as per forum debate
• Read MBIS charges from ORCA output
• Read multiple ORCA coordinate sets
• Parse NMR spectra from ORCA
• Parse ORCA electronic spectra
• Add basic support for v3000 molfiles, including for large molecules
• Small patch to parsing XYZ trajectories to handle ORCA 6 separators
• Add support for reading and writing atom force vectors
• Support reading files in UTF-16 format

🐛 Bug Fixes

• Allow surface generation to be cancelled
• Add progress bar for optimizations, including cancel
• Switch text rendering to use interpolation
• Fix code for haptic ligands. Pick the furthest dummy to attach
• Only enable the PQR search command if the site is reachable
• Tweak the centroid and center-of-mass commands
• Fix manipulate and label tools to rotate by default
• Fix right-click to delete a hydrogen and adjusting after deleting a bond
• Copy bonds and bond orders when generating super cells
• Fix parsing molecular orbital coefficients in some ORCA output files
• Handle upper-case [ATOMS] line in Molden files from Cfour
• Fix plugin downloader @matterhorn103
• Prevent a possible unhandled exception from parsing JSON
• Fix crash when creating ligands from the clipboard -- off-by-one bug
• Ensure BABEL_LIBDIR and BABEL_DATADIR are set properly on Mac
• Fix XYZ trajectories - prevent final frame with 0,0,0 coords
• Make sure the measure tool has a good contrast with background color
• Switch import format for Open Babel to CJSON if supported
• Fix perception of amide nitrogens - should be sp2-like
• Default tool wasn't set properly, so rotations, etc. ignored
• Add more error checking for Fetch PDB
• Fix bug reported in #1637 with mis-parsing selenium atoms in PDB
• Ask before re-perceiving a space group
• Switch back to importing from PDB using PDB instead of MMTF format
• Fix crash with short TER record
• Fix crash when reading cjson with invalid layer data
• Fixed Select bugs reported on forum
• Fix crash from centroids with empty molecule
• Fix crash at startup when opening a file from command-line
• Fix drag-to-install for scripts, esp. energy calculators
• App crashes when clicking "Optimize Geometry" without any atom @perminder-17
• Clarify line width / size in spectra dialog
• Add double-check for addEdge to prevent potential crash
• Ensure "split" buttons don't create a transparent background
• Use QDesktopServices on Linux too with Qt 6, which fixes opening URLs @matterhorn103
• Update desktop file name in QApplication code @matterhorn103
• Update the newer compilation guide @nbehrnd
• Export icons according to XDG icon spec on unix @matterhorn103
• Use name according to the XDG standard, harmonize metadata with flatpak @matterhorn103
• Make sure to create directories for drag-and-drop install of Python scripts
• Tweak the text and tooltips in the rendering dialog
• Fix crash when no selection is made when saving files

🚀 Performance Improvements

• Use flying edges for mesh generation @perminder-17
• When possible, load Python script names from cache
• Turn off default depth blur, shadows, edge for speed

🧰 Maintenance & Build Improvements

• Updated tests to Qt6 @peach280
• Explicitly use signed char in meshgenerator to avoid narrowing error on ARM @matterhorn103
• Fix residue not initializing id in default constructor
• ENH/BUG: Code Clean Up, Optimization, Documentation @TactfulDeity
• Add flatpak workflow for GitHub Actions @matterhorn103
• Update to latest Qt patch version and install-qt-action @matterhorn103
• Set a project-wide variable for molecule data dir AvogadroLibs_SOURCE…
• Unbundle all charge and forcefield scripts
• Update comment headers to new format (missed some in prev effort)
• Use release certificate signing on Windows
• Bumping to Qt 6.8 (latest LTS) for Mac and Windows builds
• Switch AppImage build to use the new linuxdeploy tool
• Further fixes for Qt6 @matterhorn103
• Fix building Qt Plugins without spglib (USE_SPGLIB=OFF) @MehdiChinoune
• Cmake: Remove custom Find<Package>.cmake modules @LecrisUT
• Fix wrong variable name @antonio-rojas
• Fix windows debug log

📚 Translations

• Remove many incorrect "fuzzy" translations @e-kwsm
• Fix a few ellipsis inconsistencies @matterhorn103
• chore: put space after period @e-kwsm
• Automated translation updates @github-actions
• Translations update from Hosted Weblate @weblate

Credits

Thanks to many contributors, including: @Cartrigger, @LecrisUT, @MehdiChinoune, @Milziade, @NorwayFun, @RickyLam11, @SantosSi, @TactfulDeity, @TamilNeram, @ZhangHMDS, @alexrsoares, @andibing, @antonio-rojas, @dependabot, @e-kwsm, @ghutchis, @github-actions, @matterhorn103, @milotype, @nbehrnd, @ostriz2, @ovari, @peach280, @perminder-17, @rezaalmanda, @secretkontributer, @simmon-nplob, @snowcliffx, @tacitcoast, @weblate, @ykertytsky, @zhangtengshuo, Eisuke Kawashima, KeysBits, LibreTranslate, Remus-Gabriel Chelu, Weblate Translation Memory, fox and gallegonovato