Avogadro 1.103.0

🌟 Highlights (tldr)

• Switch to use OpenGL 4.0 core profile for improved rendering speed
• Volumetric rendering style for surfaces (orbitals, electron density, spin density)
• Add peptide builder
• Add keyboard shortcuts for functional groups and ligands to template tool
• Display both alpha / beta orbitals in the orbital window
• Performance optimizations for basis set calculations
• Improved heuristics for opening CIF and crystallographic files
• Update conformer plots for RMSD and energy
• Support for isotope specification for atoms
• Improved LAMMPS and Turbomole support
• Many thanks to everyone for bug reports, suggestions and ideas!

✨ Features

• Typeset the Hall symbols using HTML @ghutchis (#2572)
• Tweak the "Fill Unit Cell" and add "Fill Translational Cell" for DFT packages @ghutchis (#2571)
• Add a warning if attempting to fill a primitive cell @ghutchis (#2569)
• Allow export to the same filename (and format) from the warning dialog @ghutchis (#714)
• Re-enable JSON-RPC support @ghutchis (#699)
• Updated AutoSave Feature @ghutchis (#668)
• Add an "export graphics" toolbar button @ghutchis (#681)
• Read molfile / sdf conformers @ghutchis (#2563)
• Add support for reading elements from VASP OUTCAR formats @ghutchis (#2567)
• Volumetric rendering support @ghutchis (#2559)
• Update arrow rendering for force and dipoles @ghutchis (#2545)
• Support pdb trajectories @ghutchis (#2560)
• Migrate to OpenGL 4.0 core profile @ghutchis (#2548)
• Orbital table - add "occupation" arrows instead of status @ghutchis (#2542)
• Improved Lammps import @e-kwsm (#2504)
• feat(CrystalTools): enable rotateToStandardOrientation to convert cell to right-handed system @e-kwsm (#2492)
• Set a better default zoom for orthographic projection @ghutchis (#2480)
• Change shift modifier to twist, not twist-and-zoom @ghutchis (#2476)
• Tweak edit and template tool to rotate, etc. with modifier keys @ghutchis (#2475)
• Add imported spectra, vibrational and magnetic CD support to spectra dialog @ghutchis (#2444)
• Add support for custom residue labels @ghutchis (#2424)
• Put the axes back as a scene plugin / display type @ghutchis (#2423)
• feat(Turbomol): output $isosub @e-kwsm (#2393)
• fix(Turbomole): use $coord angs for read @e-kwsm (#2418)
• Turbomole: support $periodic @e-kwsm (#2379)
• Update Conformer plots for RMSD and Energy @ghutchis (#2382)
• Add peptide builder @ghutchis (#2351)
• Enable the XRD display from other programs (just return a spectra) @ghutchis (#2385)
• Fixes to constraints dialog @jcerezochem (#2384)

🐛 Bug Fixes

• Fix formula computation with unit cells to account for edges and corners @ghutchis (#2587)
• Use a looser criteria for detecting identical atoms with Fill Cell @ghutchis (#2578)
• Added code to handle corrupted CJSON input (#2578)
• Fix incorrect layer info in CJSON @ghutchis (#2568)
• During animation and vibrations, don't update properties frequently @ghutchis (#2536)
• Ensure end frame value is properly set in playertool @ghutchis (#2539)
• Add a guard against recursion for property tables @ghutchis (#2535)
• Use LC_NUMERIC=C for AppImage run script @ghutchis (#2533)
• Redraw the plot when changing spectra shift and offset @ghutchis (#2532)
• Re-enable editing the molecule name, broken by #2523 @ghutchis (#2531)
• Fix issues for interactive undo/redo crashes @ghutchis (#2524)
• fix(Hdf5DataFormat): fix memory leak @e-kwsm (#2511)
• Only request name updates when the dialog is open @ghutchis (#2523)
• Fix a crash when deleting atoms from an imported molecule @ghutchis (#2513)
• Fix crash when using the align tool and switching molecules @ghutchis (#2515)
• Running commands with pixi would fail because asyncExecute was called @ghutchis (#2510)
• Migrate the name code away from the model - hopefully less crash-prone @ghutchis (#2509)
• For orthographic projection go back to frustrum planes @ghutchis (#2482)
• Fix jump in light source from opaque to translucent @ghutchis (#2481)
• If we encounter a 2D molfile use the Open Babel support @ghutchis (#2464)
• Fix signal to display surfaces after generation @ghutchis (#2457)
• Ignore some Open Babel formats for writing (e.g., png, nul) @ghutchis (#2455)
• Validate colors with the color button before use (e.g., cancel) @ghutchis (#2454)
• Validate property edits to make sure inadvertent edits set to zero @ghutchis (#2450)
• Fix CML support with HDF5 data files @ghutchis (#2446)
• Fix NWChem geometry parsing @ghutchis (#2439)
• Adjust the N-H dihedral angle to work better in folded states @ghutchis (#2438)
• Ensure we can read NWChem files with lowercase element symbols @ghutchis (#2434)
• Fix import of large (>1000 atom) MOPAC aux files @ghutchis (#2426)
• Fix off-by-one MO rendering bug with MOPAC orbitals @ghutchis (#2422)
• Adjust surface generation to keep winding consistent + and - mesh @ghutchis (#2420)
• Fixed color gradient for labeling by atomic index @brockdyer03 (#2387)
• Fix reading energies in xyz files from crest @ghutchis (#2381)
• Check for a working python in the pixi env @ghutchis (#2377)
• Reject invalid bond orders in cjson @ghutchis (#2374)
• Fix reading Molden files from ORCA with spherical basis @ghutchis (#2373)
• Fix reading XYZ files with no ending newline @ghutchis (#2371)
• Fix numeric issue with centroid and center-of-mass @ghutchis (#2369)
• If pixi is available, but not a default manifest, try python @ghutchis (#2358)
• Fix a crash with reading ORCA when no MO coefficients are found @ghutchis (#2355)
• Fix zoom with orthographic projection - make sure to resetCamera @ghutchis (#688)
• Fix checking for display types - also check against names @ghutchis (#682)

🚀 Performance Improvements

• Optimizations for basis set calculations @ghutchis (#2540)

🧰 Maintenance

• Fix USE_PLOTTER to allow builds to disable JKQtPlotter and charts
• Try copying Qt6 DLLs seemingly left out of Windows installer @ghutchis (#2570)
• Add [[nodiscard]] to all read and write methods @ghutchis (#2566)
• Some packaging fixes @ghutchis (#2551)
• Make sure to include Qt6 icu.dll in Windows builds @ghutchis (#2544)
• Work to speed up Windows builds @ghutchis (#2518)
• For now, disable builds with Windows ARM @ghutchis (#2516)
• fix: correct broken links @antonkesy (#2503)
• fix: correct supportedOperations @e-kwsm (#2489)
• Use --as-is flag for pixi run to avoid environment updates @harikrishna-au (#2472)
• fix: do not discard return value of QFile::open() @e-kwsm (#2448)
• fix: add missed header inclusion @e-kwsm (#2447)
• test: refactor UffGradientTest @e-kwsm (#2494)
• refactor: tweak usage of std::max and std::min @e-kwsm (#2502)
• fix(UFF): clamp acos argument to avoid NaN @e-kwsm (#2499)
• build(python)!: change install destination @e-kwsm (#2465)
• Update installation instructions and links in README @ghutchis (#2413)
• fix: replace deprecated eigen method @e-kwsm (#2409)
• build!: drop Qt5 @e-kwsm (#2366)
• fix: use nullptr instead of 0/NULL @e-kwsm (#2365)
• AvogadroLibsConfig.cmake: Find JKQTPlotter6 @heirecka (#2357)
• Add a cache for vcpkg to speed Windows rebuilds @ghutchis (#2363)
• Fix Mac volume names and escape Windows paths @ghutchis (#2362)
• Fix release tag reference in upload action @ghutchis (#2361)
• Add a "continuous" release (prelease) and upload builds @ghutchis (#2360)
• Fix path to entitlemenets for Mac codesign @ghutchis (#2349)
• chore: fix HTML link @e-kwsm (#708)

📚 Translations

• Mark the homepage URL as non-translatable @ghutchis (#710)
• Rename View Configuration dock to better reflect its function @matterhorn103 (#482)
• Move close contact and noncovalent i18n to cpp files @ghutchis (#2558)
• Automated translation updates @github-actions[bot] (#2526)
• chore: translate Qt messages @e-kwsm (#2491)

Credits

Thanks to many contributors, including: @NorwayFun, @andibing, @antonkesy, @arifpedia, @brockdyer03, @dependabot[bot], @e-kwsm, @ghutchis, @harikrishna-au, @heirecka, @jcerezochem, @maksim2005UKR, @milotype, @weblate, Alexandre R Soares, Eisuke Kawashima, Frank Hoffmann, Javier Cerezo, Remus-Gabriel Chelu, @DJ-Aswin, @andibing, @arifpedia, @matterhorn103, @oersen, @vinayakjeet, David D., Weblate Translation Memory, dependabot[bot] and github-actions[bot]

continuous

Automated build on 2026-02-07 05:20 UTC from 2d4a3af

Avogadro 1.102.1

• This release fixes a number of bugs in the recent 1.102.0 release. Many thanks to everyone submitting bug reports!
• It also offers test releases for Linux-ARM64 and Windows-ARM64. If you try these out, please let us know your experience!

✨ Features

• Add an estimated time progress dialog, particularly for surfaces @ghutchis (#2328)

🐛 Bug Fixes

• Fix the dialog for "update available" @ghutchis (#648)
• Fix Windows uninstall script to run unattended @ghutchis (#650)
• Fix bug when file was saved even if the user hit cancel @ghutchis (#653)
• Fix a bug in Linux AppImage that prevented GAFF and MMFF94 force field optimizations
• Add some logic to handle running when the user doesn't install Python @ghutchis (#2337)
• Some fixes for the ARM64 AppImage @ghutchis (#2332)
• Fix bug in which plugin installation dialog doesn't close @ghutchis (#2331)
• Add a sanity check for OB force fields - make sure they work @ghutchis (#2327)
• Fix a bug with calling default python when pixi is not available @ghutchis (#2325)
• Fix a few bugs in the constraints dialog @ghutchis (#2324)
• For now, don't bundle pixi with the AppImage @ghutchis (#2323)

🧰 Maintenance

• Minimize code duplication with a checkout action @ghutchis (#2339)
• Update GitHub Actions to use current SHA for more secure builds @ghutchis (#2338)
• Add a Windows-ARM native build for testing @ghutchis (#2335)
• Add an ARM64 build including AppImage @ghutchis (#2326)
• Add build status badges for Linux, Windows, and macOS @ghutchis (#2318)
• Fix windows build script @ghutchis (#2315)

📚 Translations

• Automated translation updates @github-actions[bot] (#2333)

Credits

Thanks to many contributors, including: @dependabot[bot], @ghutchis, @weblate, dependabot[bot] and github-actions[bot]

Avogadro 1.102.0

🌟 Highlights (tldr)

• This release is intended as a final beta before a 2.0 stable release
• Add the popular auto optimize tool
• Updated charts, including spectra using the JKQtPlotter framework
• Both macOS and Windows releases have migrated to the new Qt6 framework
  • Windows releases are now offered in the Microsoft Store as well as signed MSIX packages
• Use pixi if available to install Python and plugins
• A pile of bug fixes, updated language translations, and more

✨ Features

• Add an "add molecule" + icon in the molecule list @Daniel-Aguila (#2285)
• Show frozen atoms or constrained bonds, atoms, torsions in the property views @ghutchis (#2279)
• Add UI support for freezing X, Y, Z axis @ghutchis (#2276)
• Update animation tool with start and end frames @ghutchis (#2058)
• Use JKQtPlotter for charts (e.g. spectra) @ghutchis (#2220)
  • Easier to save plots to graphics, SVG, or PDF including a preview
• Add wireframe style for surfaces @ghutchis (#2201)
• Add support for UFF optimization with unit cells
• Update the ORCA input generator with support for constraints and frozen XYZ atoms

🐛 Bug Fixes

• Make isoValue in Molecular Orbital window consistent with Surfaces dialog @Kcorbyerd (#2312)
• Fix selection of atoms in orthographic projection @ghutchis (#2294)
• Disable split view to prevent crashing @ghutchis (#2298)
• Fix several bugs with UFF angle gradients found with AutoOptimize (#2240)
• Don't reset the camera when switching molecules @ghutchis (#629)
• Update the about dialog to handle light-dark themes @ghutchis (#624)
• Fix File → Close behavior  @Daniel-Aguila (#623)
• Fix installation of Python with pixi, repeatedly ask @ghutchis (#2290)
• Fix overly verbose MDL / SDF debug messages about M CHG, etc. @ghutchis (#2277)
• Fix #1965 - don't create the progress box until needed @ghutchis (#2274)
• Fix crash with undo / redo from template tool @ghutchis (#2272)
• Fix the missing "close" icon for the molecule model @ghutchis (#2273)
• Fix possible crashes in cube generation due to mutex locking @ghutchis (#2267)
• Don't start the forcefield setup at launch @ghutchis (#2258)
• Fix reading MO from Molden, including correct eV conversion @ghutchis (#2237)
• Ignore the Mutex when deleting Cubes @ghutchis (#2233)
• Read and write cube data and surfaces in cjson files @ghutchis (#2230)
• Make sure to read Mulliken partial charges from fchk files @ghutchis (#2231)
• fix(XYZ): fix parser of totalEnergy @e-kwsm (#2225)
• Fix reading open-shell ORCA calculations @ghutchis (#2223)
• Check SMILES and pop up a warning if there's something wrong @ghutchis (#2206)

🚀 Performance Improvements

• Don't start the forcefield setup at launch @ghutchis (#2258)

🧰 Maintenance

• Fix incorrect usage of .empty method when .clear() was intended @ghutchis (#2295)
• add Turbomole test and improve parser @e-kwsm (#2212)
• Fix QtTesting record scripts and playback @ghutchis (#625)
• Complete the AppxManifest @ghutchis (#615)
• Adapt Flatpak manifest for VTK->JKQtPlotter transition @matterhorn103 (#609)
• fix: explicitly include <cassert> @e-kwsm (#2288)
• Compress PNG files with ImageOptim @ghutchis (#2286)
• Add some very basic quantum IO unit tests @ghutchis (#2275)
• Add calc unit tests @ghutchis (#2269)
• Add a lot more unit cell tests @ghutchis (#2271)
• Make sure to codesign all components before notarizing @ghutchis (#2259)
• Add Qt6 packages for macOS and Windows @ghutchis (#2261, #2234)
• refactor(lexicalCast)!: use std::optional for return value @e-kwsm (#2232)
• build: update path to avogadrogenerators @e-kwsm (#2197)
• fix(Variant): remove unused char member from union, and add missing template specialization for char @e-kwsm (#2216)
• Use MACOS define instead of OSX (deprecated) @ghutchis (#2214)
• Create OSSF security scorecard.yml @ghutchis (#2209)
• Drop MMTF format test since it's unsupported. @ghutchis (#2205)
• Use vcpkg to install eigen3 libarchive libxml2 and zlib @ghutchis (#2203)
• docs: fix -Wdocument @e-kwsm (#2198)
• Try using Windows vcpkg to install Eigen for Python builds @ghutchis (#2202)
• Fix minor warnings from render layout duplicate names

📚 Translations

• Translations updates from Hosted Weblate @weblate
• Automated translation updates @github-actions[bot]

Credits

Thanks to @Daniel-Aguila for their first contribution in this release!

Thanks to many contributors, including: @Daniel-Aguila, @NorwayFun, @andibing, @arifpedia, @dependabot[bot], @e-kwsm, @ghutchis, @Kcorbyerd, @maksim2005UKR, @matterhorn103, @milotype, @oersen, @tacitcoast, @weblate, David D, Eisuke Kawashima, Otto Myers, Remus-Gabriel Chelu, Weblate Translation Memory, dependabot[bot], github-actions[bot] and btbt_bt

Avogadro 1.101

🌟 Highlights (tldr)

• This release is intended to fix key problems with 1.100 on Windows (missing Open Babel) as well as on macOS 26 "Tahoe" (save dialogs)
• Should more easily find Python installs on Windows
• Added support for constraints for geometry optimizations
• Added an internal UFF implementation
• Tweaked the edit tool to adjust bond lengths when the bond order or element change via click
• A pile of bug fixes, updated language translations, and more

✨ Features

• Support for a WebMO plugin @ghutchis (#2172)
• Add a copy-as-xyz command @ghutchis (#2150)
• Add constraints to property tables & save with CJSON @ghutchis (#2118)
• Add constraints for geometry optimization @ghutchis (#2096)
• Switch template tool to use updated SVG images @ghutchis (#2075)
• Improve cp2kinput @e-kwsm (#2067)
• If a cube exists (e.g., read from a file), create a default mesh @ghutchis (#2053)
• Update the molecule UI list to include richtext formulas @ghutchis (#2028)
• Add an internal implementation of UFF @ghutchis (#1963)
• When click-to-edit bond order also adjust the bond length @ghutchis (#2012)
• When clicking to change an element, tweak the bond length too @ghutchis (#2011)
• Add more options to the GAMESS input file generator @JorgeG94 (#1986)
• Rename "Meshes" interface text to "Surfaces" @ghutchis (#2009)
• Fix reading Chemeleon exyz files with no quotes around the Lattice @ghutchis (#2001)
• Add support for "allxyz" from Orca - trajectory files @ghutchis (#1995)
• Rename Analysis menu to imperative Analyze to match others @matterhorn103 (#1978)
• Add mode numbers to Vibrational Modes table @jcerezochem (#1952)
• Recognize *.tmol as turbomole @e-kwsm (#2185)
• Recognize CONTCAR and *.vasp as VASP geometry files @e-kwsm (#2152)
• Switch molecule list to enable rich-text formulas

🐛 Bug Fixes

• Reject files with invalid cell matrix @e-kwsm (#2191)
• Try to fix extraction on Windows using tar.gz instead of zip @ghutchis (#2193)
• Tweaks to support field names from Psi4 fchk @ghutchis (#2186)
• Fix generic "archive warn" messages for the download window @ghutchis (#2183)
• Fix possible crashes reading PDB files with few residues @ghutchis (#2182)
• Add additional search paths for Python on Windows @ghutchis (#2179)
• Fix #2176 parsing files with ¹¹⁸Og and ¹¹⁹Uue @e-kwsm (#2177)
• Fix cml xmlns URI @e-kwsm (#2156)
• Fix nullptr dereference @e-kwsm (#2135)
• fix(templatetool): do not localize functional groups @e-kwsm (#2169)
• Export mol/sdf with proper header @ghutchis (#2133)
• fix(Unit Cell Editor): reject modification of cell and fractional matrices if singular @e-kwsm (#2094)
• chore(input): reduce singleStep @e-kwsm (#2093)
• Fix UFF analytical gradients @ghutchis (#2088)
• Fix some crashes exposed with fuzz testing @ghutchis (#2086)
• fix(wrapFractional): fix comparison @e-kwsm (#2080)
• Fix a bug when changing the bond order atoms wouldn't move properly @ghutchis (#2072)
• Fix crash on Linux when deleting non-hydrogen atoms @ghutchis (#2070)
• fix(cjson): fix properties parsing @e-kwsm (#2068)
• Make sure to save label options for atoms, bonds and residues @ghutchis (#2052)
• Fix bug with manual rotations around axes @ghutchis (#2016)
• Fix reading Gaussian cube - make sure to set origin correctly @ghutchis (#2000)
• Fix bug with Rename Elements window @pillose (#1989)
• Make sure to cancel "Insert SMILES" @ghutchis (#1969)
• Fix dark theme - make sure to use default text and document-close icons @ghutchis (#1967)
• Make sure to delete bonds even when "adjust hydrogens" is off @ghutchis (#1966)
• Make sure Gaussian fchk orbitals are read with eV energies @ghutchis (#1958)
• Harden file readers (from fuzz tests) @ghutchis (#1950)
• Fix minor warning about "undef" layer caused by QTAIM changes @ghutchis (#2023)
• Fix bug with fog not starting with the correct background color
• Add support for detecting theme change events - update tool icons
• When multiple files are dropped, make sure to queue them for reading
• Make sure to get the correct preferred language on Mac
• Ensure the display type list is sorted

🧰 Maintenance

• Update/correct/improve Linux metainfo, including release notes @matterhorn103
• Initial support for an isApplicable scene plugin method @ghutchis (#2029)
• refactor: use string literals @e-kwsm (#2141)
• Fix typos @e-kwsm (#2122)
• Add missing spaces, and remove trailing newlines and spaces before tabs @e-kwsm (#2101)
• style: remove redundant inline specifiers @e-kwsm (#2099)
• refactor: use std::clamp (C++17) @e-kwsm (#2100)
• Style: run clang-format @e-kwsm (#2065)
• Fixed [Build] link address @todbadrakh (#2031)
• refactor(FindOpenBabel3): improvement @e-kwsm (#2024)
• Re-enable CJSON conformer unit test @ghutchis (#2192)
• build(VTK): support VTK 9 @e-kwsm (#2161)
• fix(QtOpenGL): honor QT_VERSION @e-kwsm (#2154)
• refactor: avoid strncmp @e-kwsm (#2142)
• refactor: use hypot @e-kwsm (#2131)
• refactor: use std::exchange (C++14) @e-kwsm (#2130)
• Switch to using subdirectories in avogadrodata @ghutchis (#2085)
• fix override specification @e-kwsm (#2079)
• fix: fix test suite names @e-kwsm (#2078)
• chore: remove ENABLE_TRANSLATIONS that is no longer used @e-kwsm (#2077)
• Compress SVG icons using svgcleaner @ghutchis (#2074)
• Update GitHub builds with latest Windows and Qt versions @ghutchis (#2063)
• Fix ODR violations, move enums into class scope @PPN-SD (#2059)
• Bundle libssl and libcrypto with AppImage @matterhorn103 (#2061)
• Use system eigen when building for Linux (inc. AppImage) @ghutchis (#2054)
• Resolve compiler warnings: member initialisation, variable shadowing, fallthrough, and unused variables @rrsathe (#2038)
• Enable musl linux Python wheels @ghutchis (#2047)
• Update cibuildwheel @ghutchis (#2010)
• build: remove unused Qt5LinguistTools @e-kwsm (#2041)
• test: enable spacegrouptest only if USE_SPGLIB is true @e-kwsm (#2030)
• Update find_dependency calls for Qt6 @ghutchis (#2026)
• build: bump cmake_minimum_required @e-kwsm (#2022)
• Migrate QTAIM and Symmetry to Qt6 @ghutchis (#1998)
• Set USE_MMTF to OFF by default @matterhorn103 (#2005)
• build: replace FindPythonInterp with FindPython3 @e-kwsm (#1976)
• Update CJSON to use new .contains() syntax @ghutchis (#1947)

📚 Translations

• Automated translation updates @github-actions[bot]
• i18n: resolve conflict with weblate @e-kwsm (#2097)
• style(i18n): add --check=ellipsis-unicode for gettext and use unicode ellipsis @e-kwsm (#1977)

Credits

Thanks to many contributors, including: @CubeXtreme, @DGC0LS13, @JorgeG94, @Maetnicio, @NorwayFun, @PPN-SD, @Ricky-Tigg, @SantosSi, @TamilNeram, @Yeims20, @andibing, @dependabot[bot], @e-kwsm, @ghutchis, @jcerezochem, @jeannemfavret, @kuyoeku, @matterhorn103, @milotype, @nbehrnd, @pillose, @rrsathe, @snapper764, @stokito, @tacitcoast, @todbadrakh, @weblate, Alexandre R Soares, Eisuke Kawashima, Eric Remy, Hēphaïstos, LibreTranslate, Remus-Gabriel Chelu, Weblate Translation Memory, dependabot[bot], github-actions[bot], gmkeebiy, nicejammer, Илья Рябов and Максим Горпиніч

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 (#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

Avogadro 1.99.0

🌟 Highlights (tldr)

• Further improvements to the new optimization framework, including default integrated Open Babel force fields (MMFF94, UFF, GAFF)
• New toolbar icons with light / dark theme from @matterhorn103
• Significantly faster molecular and orbital surfaces
• Vibrational spectra plotting
• Support for installing Python packages with plugins via pip or conda
• Improved selection of conda environments
• Conformer search dialog through Open Babel
• Improved template tool for inserting ligands and functional groups
  • Significant improvements from @nbehrnd for the ligand library
• Logging debugging / error messages to a file for Windows users

✨ Features

• Add optional energy / optimize code that links Open Babel @ghutchis (#1591)
• Update tool plugins to set icon as light / dark theme @ghutchis (#1578)
• Modern tool icons @matterhorn103 (#1576)
• Add confirmation dialog to install with conda or pip @ghutchis (#1559)
• Add support for first launch dialog and conda environments @ghutchis (#1562)
• Add red = a, blue = b, green = c color axes for unit cells @ghutchis (#1542)
• Vibrational spectra plot @ghutchis (#1429)
• Add UniqueID atom label type @ghutchis (#1569)
• Add ethylene, ethyne, and phosphate standard functional groups @ghutchis (#1557)
• Improved python configure dialog @ghutchis (#1555)
• Adding support for bond label in base classes and CJSON @ghutchis (#1495)
• Add "…" indicator for display types with settings @ghutchis (#1541)
• Split ligands and functional groups in the template tool @ghutchis (#1516)
• Added copy and export feature to property tables @Surajjalpun2002 (#1515)
• Add initial support for copy from tables @ghutchis (#1506)
• Add conformer search box @ghutchis (#1507)
• Allow scripts to add properties (orbitals, vibrations, cubes) @ghutchis (#1479)
• Add support for navigator commands - rotate, translate, zoom @ghutchis (#1472)
• Add template library to insert ligands or functional groups @ghutchis (#1456)
• Add support for Hall number and space group to CJSON read/write @ghutchis (#1440)
• Add new MessagePack version of CJSON @ghutchis (#1452)
• Add a message handler to grab debug / warnings on Windows @ghutchis
• Save and load the camera modelView and projection matrix @ghutchis

🐛 Bug Fixes

• Fixed typo in setDefaultPythonInterpretor() @matterhorn103 (#1583)
• Fix Mac builds @ghutchis (#1522)
• Fix quantum surface max cutoff for diffuse functions @ghutchis (#1556)
• Change "Insert fragment" ⇒ "Insert molecule" by popular request @ghutchis (#1519)
• Fix parsing XYZ files with tabs between columns @ghutchis (#1513)
• Fix bug with incorrect Unicode characters added to labels @ghutchis (#1588)
• Fix for Wayland @matterhorn103 (#1577)
• Fixed crash with angle properties on an empty molecule @secretkontributer (#1566)
• Fix density color crash @ghutchis (#1537)
• Fix crash in forcefields - check if method is valid before using it @ghutchis (#1526)
• Fix for first item in ordered plugin dialog being empty @matterhorn103 (#1523)
• Fix crash with "copy as" and an empty molecule @ghutchis (#1521)
• Turn off Color Opacity Map unless a VTK widget is active @ghutchis (#1509)
• Make sure to automatically load the "Meshes" display type @ghutchis (#1508)
• If no partial charges are assigned, set them @ghutchis (#1502)
• Fix potential crashes in selection commands @ghutchis (#1499)
• Fix vibration animation @ghutchis (#1487)
• Generate the density matrix if needed for the electron density surface @ghutchis (#1482)
• Fix empty window showing up for commands without an option dialog @ghutchis (#1468)
• Save partial charges and properly read them from CJSON @ghutchis (#1467)
• Don't show PNG files in the filter dialog @ghutchis (#1462)
• Fix GFN-FF energy - redirect GFN-FF output through a hack @ghutchis (#1454)
• Fixup PDB reading with non-standard MD files (no element column) @ghutchis (#1450)
• Fix atomic numbers from Orca - it would read electrons not symbols @ghutchis (#1451)
• Fix linear molecular template @ghutchis (#1474)
• Avoid segfaulting while manipulating carbon bonds/hydrogens @Makiah (#1493)
• Reduce ambiguity of "Export" toolbar button @matterhorn103 (#442)
• Ensure that title bar correctly displays active molecule file @Makiah (#440)

🐍 Scripting / Plugin Improvements

• Windows: Standardize plugin location based on forum feedback @ghutchis (#1605)
• Add some additional Python classes including cjson and connect @ghutchis (#1427)
• Always supply cjson to scripts @ghutchis (#1465)
• If userOptions specifies an order, use that to sort the form @ghutchis (#1503)
• Check script --menupath for {} priority numbers @ghutchis (#1501)
• Add a "text" option for scripts to add text labels / help @ghutchis (#1488)

🚀 Performance Improvements

• Skip calculating orbital / surface points too far apart (e.g., negligible) @ghutchis (#1551)
  • Leads to 2-3x faster surface generation

🧰 Builds / Maintenance

• Package OpenSSL for Windows @ghutchis
• Update Eigen cmake header references @ghutchis (#1544)
• Add Qt6 build tests @ghutchis (#1547)
• Update to cibuildwheel for Python 3.12 @ghutchis (#1546)
• Fix include of avogadrocoreexport.h @ghutchis (#1504)
• Add specialization for char* and MatrixXf types @ghutchis (#1494)
• Install ligand and functional group fragments @ghutchis (#1460)
• Make sure to copy libopenbabel on Mac for CPack @ghutchis

📚 Translations

• Correct typo @Acylation (#1553)
• Update Australian and Canadian localization from GB version @ghutchis (#1453)
• Translations update from Hosted Weblate @weblate
• Automated translation updates @github-actions
• Fix a few remaining cases of .. instead of ellipsis character @ghutchis (#1458)

Credits

Thanks to many contributors, including: @Acylation, @Azaathooth, @IagoEmanuel15, @ImgBotApp, @Makiah, @NorwayFun, @Surajjalpun2002, @alchemistcai, @bitigchi, @dependabot, @dependabot[bot], @ghutchis, @github-actions, @hakkikonu, @imgbot, @imitrichev, @joerivan, @koenr, @matterhorn103, @nbehrnd, @ovari, @research11111, @secretkontributer, @tacitcoast, @weblate, Alejandro Díaz-Moscoso, Eisuke Kawashima, Ivanushka, LibreTranslate, Remus-Gabriel Chelu, Weblate Translation Memory and gallegonovato

Avogadro 1.98.1

This is a bug-fix release, particularly for Windows users, removing a filename filter that affected opening and saving files.

This also includes the openbabel-3.dll which was left out of Windows releases.

🐛 Bug Fixes

• Make sure to grab openbabel*.dll on Windows package @ghutchis
• Migrated typedefs and changed const to constexpr @Atharva-Kanherkar (#1395)
• Fix Python module install dir @antonio-rojas (#1413)
• Revert validation of filenames. @ghutchis (#1433)
• Parsing orca output would crash when swapping orbitals @ghutchis (#1422)

🧰 Maintenance

• Add workflow concurrency - should stop builds during quick changes @ghutchis (#1418)
• vtk: Add missing OpenGL link target @antonio-rojas (#1412)

📚 Translations

• Translations update from Hosted Weblate @weblate (#1425)
• Automated translation updates @github-actions (#1424)

Credits

Thanks to many contributors, including: @Atharva-Kanherkar, @antonio-rojas, @atharrrva15, @ghutchis, @github-actions, @ovari, @weblate, Alejandro Díaz-Moscoso and Martin Slavík

Avogadro 1.98.0

🌟 Highlights (tldr)

• Integration with 3Dconnexion input devices on Mac and Windows
  • Many thanks to 3Dconnexion and Patryk Skowroński (@pskowronskiTDx) for this contribution (#1311)
• Improved rendering including ambient occlusion and real-time shadows from @aerkiaga
• New template tool for assembly of inorganic complexes and ligands or attaching functional groups (e.g, "click to add phenyl group") from @aerkiaga (#1075)
• New forcefield framework supporting external Python scripts (e.g., XTB, ASE, ANI-2x, etc.) @ghutchis (#1370)
• Better perception of bond orders @ghutchis
• Align tool (#1364) @ghutchis
• Manual translate / rotate dialog
• Fetch molecule names from PubChem, including markup
• Commands to create centroid and center-of-mass points
• Improved “fill unit cell” (#1375)
• Preview images of insert molecule fragments and import crystals
• Build improvements, including initial support for Qt6 and VTK9 fixes @cryos
• Integrated Orca ouputfile support (from Orca-enhanced Avogadro) (#1326)
• Add a generic compchem output reader (i.e., should automatically handle .out and .log files) (#1347)
• Initial scripting support (e.g., used to generate preview images through a directory) (#1344)
• Several updated toolbar icons

✨ Features

• Reading Gaussian fchk vibrations when present @ghutchis (#1380)
• Add support for atom labels (e.g., C1, C2, H1…) in the coordinate editor using "L" symbol @ghutchis (#1362)
• More pybind methods and properties @ghutchis (#1342)
• Perceive bond orders when requested by Python scripts @ghutchis (#1211)
• Support for color PLY format @spotenza2016 (#1177)
• Tweak the edge detection to allow changing the strength too @ghutchis (#1140)
• Add copy as SMILES / InChI @ghutchis (#1147)
• Add atoms for selection in wireframe rendering @ghutchis (#1128)
• Grab the "markup" name from the PubChem JSON response @ghutchis (#1105)
• Estimate bond distances in template tool @aerkiaga (#1099)
• Add formal charge combobox to template tool @aerkiaga (#1090)
• Add support for undo/redo selections, including custom menu text. @ghutchis (#1056)
• Add initial crystal and space group scripting, including fillUnitCell @ghutchis (#1374)
• Initial port of align tool from Avogadro 1.x code @ghutchis (#1364)
• Add a preview panel when PNG images are present for molecules @ghutchis (#1353)
• Auto-select a format for the user @ghutchis (#1348)
• Add extension and tool register / handle commands for scripts @ghutchis (#1320)
• Add an action to create a bond between selected atoms @ghutchis (#1303)
• Add dialog for manual manipulation @ghutchis (#1289)
• Read mopac vibrations @ghutchis (#1239)
• Screen space shading @ghutchis (#1135)
• Pick a contrasting color (vs. the background) for the text @ghutchis (#1131)
• Add a copy button for molecular properties @ghutchis (#1119)
• Fetch molecule names from PubChem PUG interface @ghutchis (#1103)
• Enable Yaehmop commands - enable if in PATH @ghutchis (#1100)
• Fix template tool, add more ligands and preview @aerkiaga (#1097)
• Perceive bond orders @ghutchis (#1096)
• Add support for polydentate ligand templates @aerkiaga (#1080)
• Add commands for centroid and center-of-mass atoms @ghutchis (#1076)
• Initial template tool @ghutchis (#1075)
• Add default spin multiplicity methods @ghutchis (#1062)
• Initial support for total charge and spin through CJSON. @ghutchis (#1058)
• Add AltLoc support to PDB importer @aerkiaga (#1047)
• Add AltLoc support to MMTF importer @aerkiaga (#1057)

🐛 Bug Fixes

• Add molden as a possible reader for generic .out files @ghutchis (#1409)
• Fix a few UI / UX issues in the surface dialog @ghutchis (#1404)
• Fix spurious "change layer" crash with the selection tool (#1406) (#1408)
• Fix for reading imaginary vibrational frequencies in ORCA outputs. @dtelsing (#1398)
• Ensure the VTK plot widget has a minimum size @cryos (#1231)
• Add uncommon "ent" extension for PDB entries @ghutchis (#1144)
• Put charge / spin in one line with two labels @ghutchis (#1143)
• By default only enable regular cartoons @ghutchis (#1141)
• Add VTK auto-init call, which avoids VTK context error message @ghutchis (#1115)
• Fix some cases where bond order perception gave up @ghutchis (#1164)
• Fix crash reading non-standard PDB file @ghutchis (#1161)
• Tweak rendering multiple bonds, rotate 45 degree angle @ghutchis (#1191)
• Fix a few UI / UX issues in the surface dialog (#1404)
• Allow for reading imaginary vibrational frequencies in ORCA outputs. @dtelsing (#1398)
• Validating filenames before opening files for read / write @ghutchis (#1367)
• Re-enable CML fragments in case someone has old files @ghutchis (#1359)
• Don't bond Noble gases @ghutchis (#1357)
• Fix autodetect for force field with inorganic complexes @ghutchis (#1337)
• Give better warnings when scripts do not load @ghutchis (#1336)
• Cleanup label serialize, fixing a potential crash @ghutchis (#1332)
• Adjust nitrogen valence determination @ghutchis (#1330)
• Fix #1317 - editor wasn't using the format specification for parsing @ghutchis (#1327)
• Fix #1179 (finally) setting the colors and transparency of MO @ghutchis (#1300)
• Add OpenSSL support on Windows @ghutchis (#1273)
• Update parsing GAMESS coordinates to store the final version @ghutchis (#1276)
• When deleting an atom, properly adjust the hydrogens of the neighbors @ghutchis (#1236)
• When removing an atom, remove bonded hydrogens if needed @ghutchis (#1230)
• Fix atom index labels to start with 1, not zero, as users expect @ghutchis (#1229)
• Fix POV-Ray mesh export @ghutchis (#1180)
• Fix requests to the NIH resolver to use new scheme @ghutchis (#1158)
• Fix editor smooth drag @ghutchis (#1157)
• Mitigate bright edges in SSAO @aerkiaga (#1148)
• Fix mis-translated export dialog @ghutchis (#1133)
• Fix colormap vtk action @ghutchis (#1145)
• Fix rendering bug that dropped half of the MO rendering @ghutchis (#1146)
• Fix bug with "combined rows" like Theory / Basis set @ghutchis (#1136)
• Catch exceptions thrown by mmtf:decode @ghutchis (#1132)
• Make sure to add / adjust valence in the correct order @ghutchis (#1112)
• Don't "apply layer" if layer is already zero @ghutchis (#1108)
• Fix bug to allow editing atom formal charges @ghutchis (#1091)
• Fix properties menu priorities @ghutchis (#1079)
• Fix some Edit and Build menu priorities @ghutchis (#1078)
• Avoid using QWheelEvent::pixelDelta() on X11 @aerkiaga (#1065)
• Fix bug selecting incorrect angle and torsion atoms @ghutchis (#1063)

🚀 Performance Improvements

• Switch to (fixed) faster dihedral formula @ghutchis (#1315)
• Fix editor smooth drag @ghutchis (#1157)
• Use singleton shaders @ghutchis (#1156)
• Make sure to cache icons for the LayerModel @ghutchis (#1152)
• Optimize NeighborPerceiver @aerkiaga (#1061)

🧰 Maintenance

• Move arc and quad mesh and linestrip convenience classes @ghutchis (#1068)
• fix typos and punctuation inconsistency (... vs …) @e-kwsm (#1046)
• Modernize Eigen3, GLEW and OpenGL use as imported targets @cryos (#1267)
• CMake modernization @cryos (#1264)
• Remove the ProtoCall code from the repository @cryos (#1260)
• Remove the MongoChem plugin from the project @cryos (#1256)
• ImportPQR should not delete the molecule! @cryos (#1250)
• Port the OpenBabel plugin to work with Qt 6 @cryos (#1248)
• VTK charts @cryos (#1247)
• CMake modernization @cryos (#1246)
• Qt6 porting @cryos (#1241)
• CMake VTK updates @cryos (#1228)
• chore: fix typos and spelling inconsistency @e-kwsm (#1174)
• Make Python bindings build as a standalone project @yurivict (#1198)
• Switch to using CJSON as the default format with obabel @ghutchis (#1378)
• Fix the AppImage build for a newer base ubuntu @ghutchis (#1339)
• CMake: Allow using externally-provided libraries @berquist (#1286)
• Add arm64 Python wheel builds for Mac @ghutchis (#1281)
• Now uses notarization for Mac builds @ghutchis (#1244)
• Now uses a CodeQL scanning workflow @ghutchis
• Avoid ambigous definition of mmtf's is_polymer @StefanBruens (#1209)
• Turn off deprecated declarations (e.g., Qt 5.15) @ghutchis (#1142)
• Fix to use "eta" filenames for "C" locale @ghutchis (#1102)
• Add Dependabot update checks for GitHub actions @ghutchis (#1083)

📚 Translations

• i18n: fixed & added russian translations @anmorgunov (#1137)
• support C locale @balducci (#1101)
• Many, many translations updates from Hosted Weblate @weblate
• Strong translations in English, Esperanto, French, Georgian, German, Hungarian, Japanese, Korean, Portuguese, Serbian, Spanish, and Turkish.

Credits

Thanks to many contributors, including: @DDinghoya, @DasJott, @Lisapple, @M3CG, @NorwayFun, @OfficerBrasidas, @SantosSi, @StefanBruens, @Surajjalpun2002, @WilliamBeltranC, @Xav83, @adityaomar3, @aerkiaga, @ahenao, @anmorgunov, @awvwgk, @balducci, @berquist, @comradekingu, @cryos, @dependabot, @dominikflorjan, @dtelsing, @e-kwsm, @ghutchis, @github-actions, @grsousajunior, @hgokhanb, @koenr, @matterhorn103, @mck89, @milotype, @nbehrnd, @nicolazanna, @ovari, @pskowronskiTDx, @salif, @simmon-nplob, @spotenza2016, @tacitcoast, @tictactoe101, @trollixx, @vamsibarnala, @weblate, @yurivict, Ajith, Alejandro Díaz-Moscoso, Alex B, Eisuke Kawashima, FAN JI, Hugel, Jörg S, Kateryna Golovanvoa, Patryk Skowroński, Shusong Zhang, Weblate Translators, gallegonovato and victor dargallo

Avogadro 1.97.0

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