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

Avogadro 1.96.0

Changes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and 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

As part of this release, we have an official AppImage build for Linux, as well as a code-signed release for macOS.

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.

✨ Features

• Insert DNA/RNA dialog @ghutchis (#909)
• Render close contacts @aerkiaga (#898)
• Create new layer from selection @ghutchis (#899)
• Tweak the mesh lighting .. now lights "from the top" @ghutchis (#880)
• Add an initial config widget to set mesh colors and opacity @ghutchis (#877)
• Import and retain space group information @ghutchis (#875)
• Write Gaussian cube files @ghutchis (#873)
• Add plugin to focus or unfocus selection @aerkiaga (#868)
• Implement close contact perception logic @aerkiaga (#862)
• Add formal charge to atom property tables @ghutchis (#839)
• Add support for formal charges @aerkiaga (#831)
• Add setting to reverse direction of scroll-to-zoom @ghutchis (#778)
• Tweak icons for label editor and selection @ghutchis (#776)
• Add tooltips to tools @ghutchis (#777)
• Add label editor to create custom labels @serk12 (#740)
• Add a copy graphics action

🚀 Performance Fixes

• Subgraph rewrite @aerkiaga (#878)
• Approximate cartoon B-spline from a small local neighborhood @aerkiaga (#860)
• Bond graph optimization @aerkiaga (#832)
• Faster bond perception @aerkiaga (#829)
• Optimize secondary structure @aerkiaga (#833)

🐛 Bug Fixes

• Add .cjson extension to files if none is present
• Update atomic masses @ghutchis (#894)
• Fix layer memory crash @ghutchis (#876)
• Fix memory leak with OpenGL: Detaching and deleting shaders/programs on updates @octycs (#855)
• Remove call for Core::Molecule rendering to eliminate casting @ghutchis (#871)
• Fix reading generic file formats with Open Babel @ghutchis (#848)
• Fix erratic editing behavior @aerkiaga (#819)
• Solve problems writing files with no extension @ghutchis (#835)
• Convert 2-letter PDB symbols to appropriate case @aerkiaga (#830)
• Fix Manipulation and Bond Centric Manipulation tools @aerkiaga (#825)
• Fall back to Wikipedia method for dihedral angles @ghutchis (#808)
• Be careful about assign or copy from molecules with no layers @ghutchis (#806)
• Disable dynamic bonding during animation @ghutchis (#767)
• Try to use 'python' in the path as a fallback @ghutchis (#746)

🧰 Maintenance

• Fix Valgrind uninitialized errors @aerkiaga (#887)
• Add tests using various sanitizers @ghutchis (#888)
• Make sure to sign and notarize the Mac build @ghutchis (#893) (#885)
• Only build overlayaxes if USE_OPENGL is enabled @ghutchis (#879)
• Try using Windows 2019 to build wheels @ghutchis (#861)
• Create Codacy scans @ghutchis (#850)
• test ">=0" within machine precision (>-EPS) @drew-parsons (#813)
• Add defaultBehavior method to render plugins @serk12 (#807)
• Update setup.py with long description from README.md and URLs @ghutchis (#750)

📚 Translations

• Translations update from Hosted Weblate @weblate
• Automated translation updates @github-actions (#853)
• Minor tweaks to the automated pull request @ghutchis (#761)

Credits

Thanks to many contributors, including: @HoangTuan110, @Lisapple, @M3CG, @SantosSi, @aerkiaga, @comradekingu, @drew-parsons, @ejatjon, @ersen0, @ghutchis, @github-actions, @github-actions[bot], @milotype, @nicolasfella, @octycs, @ovari, @rezaalmanda, @serk12, @urkawa, @weblate, J. Lavoie, Pa, Temuri Doghonadze, phlostically and 刘韬

Avogadro 1.95.1

This release fixes several bugs in the recent 1.95.0 release and is recommended for all users.

Thanks to @drew-parsons and @yurivict for prompt bug reports!

🐛 Bug Fixes

• Fix disabled "Balls and Sticks" rendering on a fresh install @serk12 (#744)
• Fix for loading settings @serk12 (#732)
• Add "..." to all input generators to indicate opening a dialog @ghutchis (#743)
• Fix reference axes menu item @ghutchis (#705)
• Continue rendering cartoons even if residues aren't found @ghutchis (#736)
• Enable script formats like cclib to ask for bond perception on read @ghutchis (#738)

✨ Features

• Initial display-only property tables @ghutchis (#711)
• Improve selection tool for layers @serk12 (#729)

🧰 Maintenance

• Make sure to run tests in avogadrolibs (including some fix for test failures) @ghutchis (#739)

📚 Translations

• Translations update from Weblate @weblate (#721)

Credits

Thanks to many contributors, including: @drew-parsons, @ghutchis, @mrmrcl, @ovari, @serk12 @yurivict, and @weblate

Avogadro 1.95.0

Changes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements.
Thanks to many for suggestions, bug reports, and discussions.

This release includes many new features, including new protein ribbon / cartoon renderings and the new "Layer"
system as part of Google Summer of Code by @serk12.

Draft developer documentation can be found at https://two.avogadro.cc

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.

We anticipate several more releases over fall 2021 as we finish up our 2.0 release.

✨ Features

• New "Layer" system, including custom rendering, locking and hiding parts of the molecule @serk12 (#709)
• Atom and residue labels @serk12 (#715)
• New protein cartoon / ribbon display @serk12 (#660 #694 #716)
• Update render options for Wireframe and Ball-and-Sticks @ghutchis (#700 #720)
• Use MMTF downloads - more efficient than PDB format @ghutchis (#699)
• Add back support for importing crystals @ghutchis (#658 #659)
• Add CJSON support for save/load residues and atom colors @ghutchis (#646)
• Refactor of Python command and input generators, including tabs @ghutchis (#667)
• New View => Apply Colors menu @ghutchis (#640 #723)
• Apply color schemes for residues @ghutchis (#638 #688)
• Add more selection commands, including select by residue @ghutchis (#632 #634)
• Render selected atoms in VdW and licorice modes @ghutchis (#702)
• Detect secondary structure from residues / backbones @ghutchis (#685)
• Save enabled / disabled state of scene / rendering plugins on quit @ghutchis
• Should now download and install translations for @ghutchis

🐛 Bug Fixes

• Fix Mac builds by turning off COORDGEN library @ghutchis (#606)
• Fix Windows installer to include all needed files @ghutchis
• Save projection type on close #682 @ghutchis
• Add a pass to fix OB plugin library paths on Mac @ghutchis (#627 #628)
• Fix odd behavior on 'Center' command @serk12 (#728)
• Fix several crashes with proteins @ghutchis (#724 #726 #727)
• Fix crash in CJSON reading file without labels @ghutchis (#722)
• Fix bug deleting selected atoms #650 @ghutchis (#672 #677)
• Fix "delete last atom" bug @ghutchis (#691)
• When dragging to create a new atom, use starting coords @ghutchis (#690)
• Fix #679 - incorrect PDB unit cells @ghutchis (#689)
• Fixed problems inserting SMILES without coordinates @ghutchis (#661)
• Fix for transparent widgets @ghutchis (#656)
• Fix #602 - use Molden order for f-orbitals @ghutchis (#649)
• If a chain ID is missing / invalid, skip (to read non-standard PDB) @ghutchis (#647)
• Make sure to reset colors when changing elements @ghutchis (#708)

🧰 Maintenance

• Make sure to install crystals directory even when it exists @ghutchis (#613)
• Replace NULL/0 with nullptr @e-kwsm (#617)
• Add support for reading partial charge models from obabel @ghutchis (#626)
• Replace obsolescent LINK_(PRIVATE|PUBLIC) with (PRIVATE|PUBLIC) @e-kwsm (#629)
• Refactor Molecules class @serk12 (#648)
• Don't install cclib script - which was removed @ghutchis (#662 #663)

📚 Translations

• Fix fuzzy entry for Nihonium (not Zirconium!) @e-kwsm (#618)
• Fix all incorrect fuzzy entries #619 @e-kwsm (#643)
• Remove wrong entries which were fuzzy @e-kwsm (#644)
• Translations update from Weblate @weblate (#625)
• Add a workflow which should update the translation template continuously @ghutchis (#624)

Credits

Thanks to many contributors, including: @12emin34, @GicoProgram, @LihanzUpenn, @NathanBnm, @San4ito, @acunm, @alexrsoares, @danialk03, @dillonschultz93, @e-kwsm, @ghutchis, @grsousajunior, @psavery, @rezaalmanda, @serk12, @tacitcoast, @weblate, Eisuke Kawashima, Jacque Fresco and phlostically

Avogadro 1.94.0

We are pleased to announce the latest release of Avogadro, including piles of
bug fixes and feature enhancements.

As part of the release, we've made it easier to download scripts and data,
including new input generators, molecule fragments, and build and analysis
commands. These scripts make it much easier to integrate Avogadro with many
open source chemistry Python tools, including RDKit, ASE, etc.

Draft developer documentation can be found at https://two.avogadro.cc

If you have comments or suggestions, please join us at https://discuss.avogadro.cc

We anticipate several more releases over the summer and early fall 2021.

Features

• Bring back "insert framgent" builder from Avogadro v1 @ghutchis (#591)
• New docs on http://two.avogadro.cc @ghutchis (#568)
• Remove dependency on MoleQueue @cryos (#596)
• Initial Flatpak package @kevinsmia1939
• Improved download widget @ghutchis (#534)
• Reorganize menus - fix #474 @ghutchis (#564)
• Export to SVG @serk12 (#588)
• Symmetry enhancements @ghutchis (#553)
• Added yaehmop with band structure calc @psavery (#339)
• Cp2k input @ghutchis (#383)
• OpenMM script builder plugin @badarsh2 (#343)
• Handle drag-and-drop of files to the window @ghutchis
• Use native message / dialog boxes on Mac @ghutchis
• Download entries from PDB @ghutchis (#575)
• Allow manipulate to rotate selected fragments @ghutchis (#594)
• Add bestFitPlane on Molecule @dvermd (#500)
• Add centerOfGeometry, centerOfMass and radius methods on Molecule @dvermd (#499)
• Reset view (camera) @serk12 (#450)
• Transparent support for ASE "extended XYZ" files @ghutchis (#603)

🐛 Bug Fixes

• Switch to using Python 3, fixing #431 @ghutchis (#462)
• Switch Open Babel calls to use CML and non-local numeric format (#471)
• Save background color across sessions and set bg alpha for export @ghutchis
• Add support for cut/copy/clear selected atoms @ghutchis (#510)
• Label toolbar windows for context menu @ghutchis
• Make sure to send Extensions the setActiveWidget call @ghutchis
• Make sure to install Qt image plugins on Mac and Windows @ghutchis
• Fix #483 through stream-specific locale @ghutchis (#549)
• Fix a pile of rendering bugs on high-res by saving viewport @ghutchis (#556)
• Adjust font size for 2D measure labels on hires screens @ghutchis (#548)
• Make sure to check movie sizes for high-dpi screens @ghutchis (#570)
• Fixes silent export on save bug #439 @anubh4v (#517)
• Switch to the navigate tool after pasting coordinates over empty @ghutchis (#593)
• Fix #571 - ensure we read Gaussian files from file, not stream @ghutchis (#592)
• Fix symmetry detection with dummy atoms (e.g, ferrocene example) @ghutchis (#595)

🐍 Python Improvements

• Add support for a JSON list of selected atoms @ghutchis (#440)
• Simplify wheel building @psavery (#520)
• Update example Avogadro RPC script @ghutchis

🧰 Maintenance

• Switch to using GitHub actions for continual builds @ghutchis (#461)
• Translations update from Weblate @weblate
• Get rid of bits/stdc++ headers - non-portable GCC header @ghutchis (#463)
• Add fedora patches @ghutchis (#460)
• Allow use of HDF5 >= 1.12.0 @berquist (#488)
• Remove exit calls from qtaim code @ghutchis (#475)
• Switch to include spglib.h with no subdir - fixes build issues @ghutchis (#533)
• Update residues from LigandExpo @ghutchis (#572)
• Make VtkPlot more object-oriented @psavery (#379)

Credits

Thanks to many contributors, including: @Andre870-hub, @ImgBotApp,
@KovalevArtem, @NathanBnm, @Padanian,
@Pietro026, @SantosSi, @SoftwareByRedline, @VeryTastyTomato, @Z-Fikar,
@Zaryob, @adreasnow, @ahmadubuntu, @akyunus, @amandadumi,
@andhikapangestu29, @anubh4v, @badarsh2, @berquist, @borisfaure,
@comradekingu, @crlambda, @cryos, @dnandz, @dvermd, @ghutchis,
@grsousajunior, @hello-malaysia, @imgbot, @joanavieira8,
@kevinsmia1939, @koffevar, @ludovicobesana, @mirosnik1, @niskala5570,
@psavery, @rezaalmanda, @serk12, @shivupa, @tacostea, @tiagomalho,
@udopton, @weblate, @willow88, @yavgech, Alex, Apostol Penkov, Editor
Do Sonic BR, Irina Puscas, J. Lavoie, Jacque Fresco, Jörg S, Kavin
Teenakul, Liu Tao, Michalis, My Random Thoughts, Oğuz Ersen, RIDHO
NURUL ADILLA, Szabolcs Kalapos, Talking Panda, Thomas Koller, Tymofij
Lytvynenko, fikril Ha, phlostically, rahul bahuguna

Avogadro Libraries 1.93.0

The latest Avogadro libraries release with a number of feature enhancements and bug fixes.