Avogadro2の旧バージョン・全バージョン一覧

We are pleased to announce the Avogadro 2.1, with new features, performance improvements, and piles of bug fixes. A particular effort was made to improve testing and code quality.

Thanks to everyone who made suggestions, bug reports, translations, and discussions. Avogadro is built from the community, and we appreciate all the help.

Avogadro v2 was designed as a platform to make it easy to build the next generation of molecular and materials visualization, including fast modern rendering and improved stability. With this release, we mark 30 plugins and will offer tutorials on making your tools easily available as plugins.

## 🌟 Highlights (tldr)
• **New Z-matrix editor**：view and edit internal coordinates, including constraints, dummy atoms for linear molecules, and drag-and-drop to reorder atoms. Input generators can now write Z-matrix coordinates.
• **Faster, smoother geometry optimization** using the ABC-FIRE method and a hybrid mode that is now the default for Optimize and AutoOpt.
• **Much faster orbitals and surfaces**：Gaussian basis set calculations are up to 20-25× faster, large ORCA files load much faster too.
• **Improved conformer and dynamics plot** including geometry parameters, velocities, temperature, etc.
• **Batch energies and forces**：recalculate energies and forces for every conformer or frame at once, in batches suited to ML potentials.
• **New building tools**
- An initial polymer builder - feedback welcome
- D-amino acids in the peptide builder.
- Edit distances, angles, and dihedrals directly in the Measure tool.
- PDB biological assemblies (tested to ~1 million atoms).
- Fractional supercells.
- Better support for CIF files, including space group perception from transforms.
• **New camera controls**：virtual trackball rotation for all tools, keyboard shortcuts for rotating, and click-and-drag to focus on an atom.
• **Custom properties**：atom, bond, residue, and conformer properties are kept and can be viewed and edited in the property tables.
• **Better vibrations**：each step of an optimization or scan can now have its own vibrations, displaced geometries can be generated, and ORCA symmetry labels are read.
• **Scripting and automation**
- Many tools can now be controlled through a JSON-RPC interface, including selection, measurement, force fields, constraints, symmetry, spectra, colors, and hydrogens.
- The `avogadro.connect` Python module can now list the available commands, making it easy to drive Avogadro from Jupyter, scripts, or AI agents.
- A new `avogadro-mcp` project for connecting local LLM models and agents to Avogadro.
• **Transparent compression support** read and write compressed files directly (e.g., `.gz`, `.xz` and `.zstd`).
• **Plugin improvements**：progress bars and a cancel button for plugin scripts, plus authors, download counts, and bug tracker links in the plugin window. Installs are more reliable.
• **More stable**：continuous fuzz testing on Linux and Windows found and fixed a large number of bugs and potential crashes in file readers and editing.

## ✨ Features
• Refactor PLY export with scene tesselation @ghutchis (#3107)
• Add content patterns for file format detection @ghutchis (#3093)
• Initial support for z-matrix coordinates in input generators @ghutchis (#3015)
• Set the default filename in input generators @ghutchis (#3013)
• Add authors, download count and bug tracker link to plugin window @ghutchis (#3012)
• Add constraints to the z-matrix editor @ghutchis (#3010)
• Add support for time, velocities and temperature to the conformer chart @ghutchis (#3006)
• Add shared camera controls for all tools / modes @ghutchis (#2972)
• Add support for fractional ranges for supercells @ghutchis (#2955)
• Extend PlotConformer scan coordinate support @ghutchis (#2998)
• Add support for transparent compression IO @ghutchis (#2994)
• Allow drag-and-drop to reorder atoms in the property table @ghutchis (#2993)
• Add a z matrix editor window @ghutchis (#2990)
• Rework the internal \<=>

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements. Thanks to many for suggestions, bug reports, translations, and discussions. Avogadro is built from the community, and we appreciate all the help.

Avogadro v2 was designed for fast modern rendering and improved stability. It is a platform to make it easy to build the next generation of molecular and materials visualization and editing tools. If you haven't used an Avogadro2 beta (1.95 through 1.103) you will find many new features, performance improvements and changes.

## 🌟 Highlights (tldr)

• New plugin system will load menu commands, input generators, file formats, energy and electrostatic models, including installation of any required libraries and tools using [`pixi`](https://pixi.prefix.dev/latest/installation/) on Mac and Windows. (Highly recommended on Linux too)
• New plugin install window and index, including over 20 plugins (and growing)
- Includes a variety of ML potentials, charge assignment using AM1-BCC and ABCG2, building nanotubes and surface slabs, generating disordered ice unit cells, and many more.
- Easy to build and customize with Python - link to a wide variety of packages
• Faster geometry optimizations ~50% faster on all models, and up to 5-10x faster on large molecules using UFF.
• Added a faster protocol for using external energy models, including ML potentials, XTB, and more.
• Added a simple molecular dynamics mode to the AutoOpt tool, including with energy models.
• Improved ORCA input generator, including syntax highlighting
• [Revised, updated documentation](https://two.avogadro.cc/docs/)

## ✨ Features
• Add keyboard shortcuts for next file (`Ctrl+Tab`) and previous file (`Ctrl+Shift+Tab`) @brockdyer03 (#795)
• Add keyboard shortcuts for going forward / backwards in animations @ghutchis (#2760)
• If the molecule changes (e.g., plugin) render a new cube @ghutchis (#2731)
• Allow user-options metadata to be "dynamic" and call the script @ghutchis (#2703)
• Add support for reading from a filename (e.g., hd5 file) @ghutchis (#2695)
• Move autoopt and forcefield optimizations off the main GUI thread @ghutchis (#2700)
• For local installs, use the README @ghutchis (#2692)
• Adjust format of command script menu paths @matterhorn103 (#2682)
• fix：add label font scale setting for display customization @newtontech (#2662)
• Updated "manage plugins" interface @ghutchis (#2646)
• Update the energy-model (scriptenergy.cpp) to allow user-options @ghutchis (#2660)
• Enable user-options for commands and input-generators to be TOML files @ghutchis (#2643)
• Update plugin installer for packages @ghutchis (#2639)
• Implement new plugin framework @ghutchis (#2626)
• Add faster scriptenergy protocol @ghutchis (#2621)
• Allow a context menu to select the partial charge model @ghutchis (#2609)
• Add write support for molden @ghutchis (#2602)
• Add simple molecular dynamics @ghutchis (#2527)
## 🚀 Performance Improvements
• Update the binary protocol for energy+grad and Hessian @ghutchis (#2699)
• Refactor to use newest cppoptlib (C++17) and make it private @ghutchis (#2697)
• Improve latency with binary mode @ghutchis (#2667)
• Add faster scriptenergy protocol @ghutchis (#2621)
## 🔌 Plugins
• Add more syntax highlighting options and add support for dark mode. @brockdyer03 (#2709)
• Clean the pixi cache every 30 days @ghutchis (#782)
• Add support for removing old plugins on first launch @ghutchis (#775)
• Update plugin installation message @ghutchis (#765)
• Add code to load new packages out of directories for install @ghutchis (#739)
## 🐛 Bug Fixes
• Parse PDB space group from CRYST1 record @ghutchis (#2771)
• Make sure to clear old cubes and meshes when generating VdW, etc. @ghutchis (#2769)
• Fix default colors for spectra dialog to be dark/light theme aware @ghutchis (#2767)
• Make sure to capture the FBO before initialize @ghutchis (#2768)
• Use bold font for active file or layer - works bet

🌟 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
- Add support for reading and rendering DNA / RNA backbones
- Improve python selection dialog
- Calculate and render dipole moments
- Edit molecule name, charge, and spin in properties
- Improve manipulate dialog - rotate around origin, molecule center, selection center
- Update the template tool to place ligands or functional groups
- Support for additional secondary structures (3-10 and pi helix) @TactfulDeity
- Implement g orbitals
- cp2kinput improvements @e-kwsm
- Add support to render atomic partial charge labels
- Add support to render bond lengths
- Add HOMO and LUMO energies to molecular properties
- Add Shortcut Keys to navigate/modify tools (Issue #1794) @Milziade
- Add "change elements" dialog
- Editing molecular charge / spin => input generators and plugins
📄 File Format Improvements:
- Parse inputParameters if present in cjson
- Read radicals from SDF / Molfile
- Parse more MOPAC aux properties including coordinates
- Parse CHELPG charges from ORCA output too
- Export to XYZ format with 10 decimal precision as per forum debate
- Read MBIS charges from ORCA output
- Read multiple ORCA coordinate sets
- Parse NMR spectra from ORCA
- Parse ORCA electronic spectra
- Add basic support for v3000 molfiles, including for large molecules
- Small patch to parsing XYZ trajectories to handle ORCA 6 separators
- Add support for reading and writing atom force vectors
- Support reading files in UTF-16 format
🐛 Bug Fixes
- Allow surface generation to be cancelled
- Add progress bar for optimizations, including cancel
- Switch text rendering to use interpolation
- Fix code for haptic ligands. Pick the furthest dummy to attach
- Only enable the PQR search command if the site is reachable
- Tweak the centroid and center-of-mass commands
- Fix manipulate and label tools to rotate by default
- Fix right-click to delete a hydrogen and adjusting after deleting a bond
- Copy bonds and bond orders when generating super cells
- Fix parsing molecular orbital coefficients in some ORCA output files
- Handle upper-case [ATOMS] line in Molden files from Cfour
- Fix plugin downloader @matterhorn103
- Prevent a possible unhandled exception from parsing JSON
- Fix crash when creating ligands from the clipboard -- off-by-one bug
- Ensure BABEL_LIBDIR and BABEL_DATADIR are set properly on Mac
- Fix XYZ trajectories - prevent final frame with 0,0,0 coords
- Make sure the measure tool has a good contrast with background color
- Switch import format for Open Babel to CJSON if supported
- Fix perception of amide nitrogens - should be sp2-like
- Default tool wasn't set properly, so rotations, etc. ignored
- Add more error checking for Fetch PDB
- Fix bug reported in #1637 with mis-parsing selenium atoms in PDB
- Ask before re-perceiving a space group
- Switch back to importing from PDB using PDB instead of MMTF format
- Fix crash with short TER record
- Fix crash when reading cjson with invalid layer data
- Fixed Select bugs reported on forum
- Fix crash from centroids with empty m