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Avogadro 1.100.0

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@github-actions github-actions released this 22 Jan 01:15
· 19 commits to refs/heads/master since this release
1.100.0
7c04f64

🌟 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