github-actions
released this
22 Jan 01:15
·
19 commits
to refs/heads/master
since this release
🌟 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 (#1874)
- Add support for reading and rendering DNA / RNA backbones (#1831)
- Improve python selection dialog (#1844)
- Calculate and render dipole moments
- Edit molecule name, charge, and spin in properties (#1810)
- Improve manipulate dialog - rotate around origin, molecule center, selection center (#1774)
- Update the template tool to place ligands or functional groups (#1777)
- Support for additional secondary structures (3-10 and pi helix) @TactfulDeity (#1746)
- Implement g orbitals (#1826)
- cp2kinput improvements @e-kwsm (#1702)
- Add support to render atomic partial charge labels (#1726)
- Add support to render bond lengths (#1871)
- Add HOMO and LUMO energies to molecular properties (#1803)
- Add Shortcut Keys to navigate/modify tools (Issue #1794) @Milziade (#1807)
- Add "change elements" dialog (#1863)
- Editing molecular charge / spin => input generators and plugins
📄 File Format Improvements:
- Parse inputParameters if present in cjson (#1849)
- Read radicals from SDF / Molfile (#1848)
- Parse more MOPAC aux properties including coordinates (#1843)
- Parse CHELPG charges from ORCA output too (#1829)
- Export to XYZ format with 10 decimal precision as per forum debate (#1824)
- Read MBIS charges from ORCA output (#1823)
- Read multiple ORCA coordinate sets (#1808)
- Parse NMR spectra from ORCA (#1799)
- Parse ORCA electronic spectra (#1797)
- Add basic support for v3000 molfiles, including for large molecules (#1765)
- Small patch to parsing XYZ trajectories to handle ORCA 6 separators (#1705)
- Add support for reading and writing atom force vectors (#1674)
- Support reading files in UTF-16 format
🐛 Bug Fixes
- Allow surface generation to be cancelled (#1894)
- Add progress bar for optimizations, including cancel (#1893)
- Switch text rendering to use interpolation (#1917)
- Fix code for haptic ligands. Pick the furthest dummy to attach (#1916)
- Only enable the PQR search command if the site is reachable (#1892)
- Tweak the centroid and center-of-mass commands (#1891)
- Fix manipulate and label tools to rotate by default (#1861)
- Fix right-click to delete a hydrogen and adjusting after deleting a bond (#1896)
- Copy bonds and bond orders when generating super cells (#1898)
- Fix parsing molecular orbital coefficients in some ORCA output files (#1899)
- Handle upper-case
[ATOMS]
line in Molden files from Cfour (#1785) - Fix plugin downloader @matterhorn103 (#1767)
- Prevent a possible unhandled exception from parsing JSON (#1742)
- Fix crash when creating ligands from the clipboard -- off-by-one bug (#1739)
- Ensure BABEL_LIBDIR and BABEL_DATADIR are set properly on Mac (#1736)
- Fix XYZ trajectories - prevent final frame with 0,0,0 coords (#1720)
- Make sure the measure tool has a good contrast with background color (#1718)
- Switch import format for Open Babel to CJSON if supported (#1707)
- Fix perception of amide nitrogens - should be sp2-like (#1652)
- Default tool wasn't set properly, so rotations, etc. ignored (#1647)
- Add more error checking for Fetch PDB (#1646)
- Fix bug reported in #1637 with mis-parsing selenium atoms in PDB (#1643)
- Ask before re-perceiving a space group (#1639)
- Switch back to importing from PDB using PDB instead of MMTF format (#1642)
- Fix crash with short TER record (#1640)
- Fix crash when reading cjson with invalid layer data (#1636)
- Fixed Select bugs reported on forum (#1625)
- Fix crash from centroids with empty molecule (#1624)
- Fix crash at startup when opening a file from command-line (#1621)
- Fix drag-to-install for scripts, esp. energy calculators
- App crashes when clicking "Optimize Geometry" without any atom @perminder-17 (#1661)
- Clarify line width / size in spectra dialog (#1678)
- Add double-check for addEdge to prevent potential crash (#1704)
- 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 (#1741)
- When possible, load Python script names from cache (#1830)
- Turn off default depth blur, shadows, edge for speed (#1728)
🧰 Maintenance & Build Improvements
- Updated tests to Qt6 @peach280 (#1941)
- Explicitly use signed char in meshgenerator to avoid narrowing error on ARM @matterhorn103 (#1842)
- Fix residue not initializing id in default constructor (#1786)
- ENH/BUG: Code Clean Up, Optimization, Documentation @TactfulDeity (#1779)
- Add flatpak workflow for GitHub Actions @matterhorn103 (#1772)
- Update to latest Qt patch version and install-qt-action @matterhorn103 (#1841)
- Set a project-wide variable for molecule data dir AvogadroLibs_SOURCE… (#1851)
- Unbundle all charge and forcefield scripts (#1832)
- Update comment headers to new format (missed some in prev effort) (#1828)
- Use release certificate signing on Windows (#1821)
- Bumping to Qt 6.8 (latest LTS) for Mac and Windows builds (#1751)
- Switch AppImage build to use the new linuxdeploy tool (#1775)
- Further fixes for Qt6 @matterhorn103 (#1713)
- Fix building Qt Plugins without spglib (USE_SPGLIB=OFF) @MehdiChinoune (#1671)
- Cmake: Remove custom
Find<Package>.cmake
modules @LecrisUT (#1585) - Fix wrong variable name @antonio-rojas (#1612)
- Fix windows debug log
📚 Translations
- Remove many incorrect "fuzzy" translations @e-kwsm
- Fix a few ellipsis inconsistencies @matterhorn103 (#1771)
- chore: put space after period @e-kwsm (#1697)
- 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