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