ahuelsmeier/gsl-transition-generator: GSL & Ceramide Transition Generator v1.1.0 - Release

What's New in Version 1.1.0 This is a major architectural update focused on calculation accuracy, codebase maintainability, and resolving edge-case fragmentation bugs. Bug Fixes & Chemistry Updates: Isotope Labeling Fix: Resolved a critical bug involving heavy isotope math. Fragments that lose the nitrogen atom (e.g., LCB fragmenting to lose -C2H8NO) now correctly drop the N15 label, smoothly transitioning precursors like [M2DN15-H] down to [M2D-H]. Isolated Chemistry Engine: Math and validation logic for adducts and exact masses have been completely separated, ensuring zero ghost-bugs across different lipid classes. Under-the-Hood Improvements: Modular Architecture: The massive monolithic script has been completely refactored into a modern, production-grade Python package (database.py, chemistry.py, fragment_rules.py, isotope_labeling.py). Stable GUI Bridge: The backend was entirely swapped out without altering the graphical user interface. A new router dynamically feeds configuration lists (like Standard and Deoxy LCBs) directly to the GUI. Easier Contributions: Code is now highly readable, making it much easier to add new lipid classes or tweak mass spec fragmentation rules in the future. Installation Instructions Windows Download and extract GSL-Generator-v1.1.0-Windows.zip Run GSL-Generator-v1.1.0-Windows.exe Note: The Windows executable includes all required runtime libraries. Linux Download and extract GSL-Generator-v1.1.0-Linux.zip Make executable: chmod +x GSL-Generator-v1.1.0-Linux.bin Run: ./GSL-Generator-v1.1.0-Linux.bin macOS (Untested) Download the appropriate version for your Mac Intel Macs (2020 and earlier): Use macOS-Intel version Apple Silicon (M1/M2/M3): Use macOS version Extract the zip file Open Terminal and run: cd ~/Downloads chmod +x GSL-Generator-v1.1.0-macOS.bin xattr -d com.apple.quarantine GSL-Generator-v1.1.0-macOS.bin ./GSL-Generator-v1.1.0-macOS.bin or cd ~/Downloads chmod +x GSL-Generator-v1.1.0-macOS-Intel.bin xattr -d com.apple.quarantine GSL-Generator-v1.1.0-macOS-Intel.bin ./GSL-Generator-v1.1.0-macOS-Intel.bin Note: macOS builds are automatically compiled but haven't been tested on actual hardware. Please report any issues! Features Generate transitions for GSLs (GM1, GM2, GM3, GD1a, GD1b, GT3, GQ1, etc.) Multiple adduct types and charge states Support for Ceramides and deoxyCeramides Configurable LCB chains and fatty acids Isotope labeling support (M2DN15, M3D) Positive and negative ion modes System Requirements No Python installation required - standalone executables Windows 10/11 (64-bit) or Linux (64-bit)