Metadata-Version: 2.4
Name: phenoms
Version: 0.2.2
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Rust
Requires-Dist: mdtraj>=1.9
Requires-Dist: polars>=1.0
Requires-Dist: pandas>=1.0
Requires-Dist: numpy>=1.20
Requires-Dist: matplotlib>=3.5
Requires-Dist: seaborn>=0.11
Requires-Dist: tqdm>=4.60
Requires-Dist: joblib>=1.0
Requires-Dist: scikit-learn>=1.0
Requires-Dist: networkx>=3.0
Requires-Dist: click>=8.0
Requires-Dist: mdanalysis>=2.4 ; extra == 'benchmark'
Requires-Dist: pytest>=7.0 ; extra == 'dev'
Requires-Dist: pytest-cov>=4.0 ; extra == 'dev'
Requires-Dist: sphinx>=7.0,<9 ; extra == 'docs'
Requires-Dist: shibuya>=2024.7.0 ; extra == 'docs'
Requires-Dist: myst-parser>=3.0 ; extra == 'docs'
Requires-Dist: mdanalysis>=2.4 ; extra == 'gromacs'
Requires-Dist: biopython>=1.79 ; extra == 'structure'
Provides-Extra: benchmark
Provides-Extra: dev
Provides-Extra: docs
Provides-Extra: gromacs
Provides-Extra: structure
License-File: LICENSE
Summary: Backbone H-bond network analysis for MD simulations (HDX-MS style)
Keywords: molecular-dynamics,hydrogen-bonds,HDX-MS,backbone
Author-email: Brandon Novy <bcnovy96@gmail.com>
License: MIT
Requires-Python: >=3.8
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

# PHENOMS

Python-based Hydrogen-Deuterium Exchange of Molecular Dynamics Simulations

PHENOMS analyzes backbone H-bond networks from MD trajectories for HDX-MS–style
interpretation: Rust-accelerated Baker–Hubbard detection, replicate/`ComparisonSet`
workflows, occupancy heatmaps, differential protection, and connectivity exports.

## Install

```bash
pip install phenoms
```

## Quick start

```python
from phenoms import SimulationSet, default_output_root

sim = SimulationSet(
    pdb_files=["rep1.pdb", "rep2.pdb"],
    sub_frames=100,
    output_dir=default_output_root() / "my_run",
)
sim.run()
```

A CLI is also available: `phenoms prep`, `phenoms run`, `phenoms compare`.

**Docs:** https://brandon-cole.github.io/PHENOMS/
**Source:** https://github.com/Brandon-Cole/PHENOMS

## License

MIT

