Release Notes

v1.2.1 “Visualization Optimized” (Release Date: November 23, 2024)

Improvements

  • Visualization Performance Optimization: Enhanced the visualization module to improve rendering speed and reduce memory usage, enabling smoother analysis of large AlphaFold 3 output files.

  • Stability Improvements: Addressed minor bugs and improved the stability of the visualization tools, ensuring a seamless user experience during structure analysis.

v1.2.0 “Visualization & Analysis” (Release Date: November 21, 2024)

New Features

  • Visualization Module: Introduced a powerful visualization module for AlphaFold 3 results. Users can upload output files (e.g., .pdb, .json) to analyze predictions with detailed structure displays, customizable plots, and PDF report generation.

  • Integrated Visualization: The visualization tools are now seamlessly integrated into the prediction GUI, allowing users to switch to the visualization tab immediately after predictions are complete.

  • Enhanced Output Analysis: Added an automated AlphaFold 3 output analysis system that provides streamlined insights with customizable visualizations and detailed reports.

  • Batch Prediction API Improvements: Updated the batch prediction API to support visualization integration and enhanced error handling.

v1.1.2 “Guided Installation” (Release Date: November 21, 2024)

New Features

  • Guided Installation: Introduced a new GUI-based installer to simplify the installation process. Users can now easily set up the application through step-by-step guidance.

  • CLI Launch: Added command-line interface support, allowing users to start the application or installation process directly from the command line using the afusion command.

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v1.1.1 “Debug and Docs” (Release Date: November 20, 2024)

New Features

  • Documentation Update: Created and improved project documentation, providing more detailed usage guidance and API descriptions.

Bug Fixes

  • Resolved known issues, enhancing application stability and reliability.

v1.1.0 “Console and API” (Release Date: November 19, 2024)

New Features

  • Console Output: Integrated console output functionality, allowing users to view the running process in real-time within the interface for easier tracking and debugging.

  • Batch Predictions API: Added an API for AFusion, supporting batch predictions in Python scripts, increasing automation.

Improvements

  • Performance Optimization: Improved application performance and stability, enhancing user experience.

  • Interface Enhancements: Made minor adjustments to the user interface for smoother and more user-friendly operation.

v1.0.0 “Refactor” (Release Date: November 18, 2024)

Overview

AFusion v1.0.0 has been officially released. This marks our first stable version, featuring a complete codebase refactor for improved performance and reliability.

Installation

pip install afusion

Run

afusion

Features

  • Code Refactoring: Comprehensive optimization of the codebase, improving maintainability and execution efficiency.

  • Stability Enhancements: Fixed issues from previous versions, significantly enhancing application stability.

v0.2.2 “Python Package” (Release Date: November 17, 2024)

New Features

  • Released as a Python Package: AFusion is now available as a Python package. Users can install and run it with a simple command, making it more convenient.

Installation

pip install afusion

Run

afusion

v0.2.1 “Copies” (Release Date: November 16, 2024)

New Features

  • Copy Number Specification: Users can now specify the number of copies for each sequence/entity, making it easy to create multiple copies of a sequence. Each copy can be assigned a unique ID, providing greater flexibility when setting up simulations.

  • Enhanced ID Handling: Maintained the original functionality where multiple IDs can be specified separated by commas (e.g., A,B), while adding the option to explicitly specify the number of copies, offering more customization possibilities.

Improvements

  • User Interface Improvements: Optimized the interface design to make the application more intuitive and user-friendly.

  • Performance Enhancements: Fixed minor issues to enhance stability and performance.

v0.2.0 “New Features” (Release Date: November 15, 2024)

New Features

  1. Run Completion Detection

    • Automatic Success Check: After running AlphaFold 3, the application now automatically checks whether the prediction completed successfully.

    • Output Folder Verification: Verifies the existence of the output directory named after your job (based on the name field in your input) to ensure results are generated.

    • User Feedback: Upon successful completion, a confirmation message is displayed along with the path to the results.

  2. Download Results as ZIP

    • In-App Download Option: Users can now download the prediction results directly from the app without needing to access the server filesystem.

    • Automatic Compression: Compresses the output folder into a ZIP file for quick and efficient downloads.

    • Seamless Integration: The download button appears immediately after a successful run, streamlining the workflow.

Important Notes

  • Ensure Correct Paths: Before running, double-check that all directory paths in the execution settings are accurate and accessible by the application.

  • Docker Requirements: The application runs AlphaFold 3 within a Docker container. Ensure that Docker and AlphaFold 3 are installed and properly configured on your system.

  • Permissions: The application needs appropriate permissions to read and write to the specified directories.

v0.1.1 “Flag Bucket” (Release Date: November 14, 2024)

New Features

  • Compilation Buckets Configuration

    • Custom Bucket Sizes: AFusion now supports specifying custom compilation bucket sizes introduced in AlphaFold 3. Users can define bucket sizes that match the input sequence lengths, reducing unnecessary model recompilations and improving performance.

    • Usage:

      1. Enable Custom Buckets: In the “AlphaFold 3 Execution Settings” section, check the “Specify Custom Compilation Buckets” option.

      2. Input Bucket Sizes: Provide a list of bucket sizes separated by commas in the “Bucket Sizes (comma-separated)” field, e.g., 256,512,768,1024.

      3. Run: Review the generated Docker command to confirm it includes the --buckets flag, then click “Run AlphaFold 3 Now” to execute the prediction.

    • Benefits:

      • Performance Optimization: Matching bucket sizes to input sequences minimizes padding and reduces the number of model recompilations.

      • Flexibility: Customize bucket sizes to handle a diverse range of input lengths, ensuring efficient processing.

Improvements

  • User Interface Updates: Adjusted the execution settings section to include the new compilation buckets configuration in an intuitive manner. Provided helpful tooltips and validation messages to guide users through the new settings.

v0.1.0 “First Release” (Release Date: November 13, 2024)

Overview

AFusion v0.1.0 has been released, providing a user-friendly graphical interface for AlphaFold 3. It simplifies the prediction process, making it accessible to users who are not familiar with command-line interactions.

Features

  • Intuitive Interface: Easily configure job settings, sequences, and execution parameters through a clean and modern GUI.

  • Entity Management: Add multiple entities (Protein, RNA, DNA, Ligand) with support for modifications, MSA options, and templates.

  • Dynamic JSON Generation: Automatically generates the required JSON input file for AlphaFold 3 based on user inputs.

  • Integrated Execution: Run AlphaFold 3 directly from the GUI with customizable Docker execution settings.