# Changelog

All notable changes to pocketeer will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [0.1.0] - 2025-11-13

### Added
- Initial release of pocketeer
- Core pocket detection using alpha-sphere method
- Delaunay tessellation-based geometry
- Graph-based clustering of alpha-spheres
- Volume estimation using voxel grid method with Numba JIT compilation
- Simple druggability scoring
- PDB I/O with simple parser and optional Biotite support
- CLI with Typer (built-in) and optional Rich for pretty output
- Comprehensive test suite
- Full API documentation in README

### Features
- `find_pockets()` - Main API function
<<<<<<< Updated upstream
- `view_pockets()` - Visualize detected pockets in 3D (if `atomworks` is installed)
- `load_pockets()` - Load precomputed pockets from file (JSON/PDB/TXT)
- Simple visualization and reloading workflow for pocket results
=======
>>>>>>> Stashed changes
- `AlphaSphere` and `Pocket` data types
- Multiple output formats (PDB, JSON, TXT)
- Clean, minimal dependencies (numpy, scipy, numba, typer)

### Performance
- Handles typical proteins (1000-5000 atoms) in 3-5 seconds
- Numba JIT compilation for volume calculation (fast and memory-efficient)
- Vectorized NumPy operations throughout
- First run slightly slower due to JIT compilation, subsequent runs are fast

[0.1.0]: https://github.com/cch1999/pocketeer/releases/tag/v0.1.0

