PHENOMS

Python-based Hydrogen-Deuterium Exchange of Molecular Dynamics Simulations

PHENOMS workflow

Documentation: https://brandon-cole.github.io/PHENOMS/

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. Backbone N–O is the default; all-bond mode and native traj+topology inputs are optional.

Install

Install Rust first, then:

conda env create -f environment.yml
conda activate phenoms
pip install -e .

pip install -e . builds the Rust kernel (phenoms.phenoms_hbond_rs) into the same package via maturin. Without a Rust toolchain at install time, PHENOMS falls back to MDTraj for detection.

Quick start

from phenoms import SimulationSet, ComparisonSet, default_output_root

sim = SimulationSet(
    pdb_files=["rep1.pdb", "rep2.pdb"],
    resid_range=(50, 70),
    sub_frames=100,
    output_dir=default_output_root() / "my_run",
)
sim.run()

a = SimulationSet(["a1.pdb", "a2.pdb"], sub_frames=100)
b = SimulationSet(["b1.pdb", "b2.pdb"], sub_frames=100)
cmp = ComparisonSet(a, b, label_a="apo", label_b="holo")
a.run(); b.run()
cmp.compare()
cmp.export_comparison_artifacts(default_output_root() / "comparison")

CLI (optional): phenoms prep, phenoms run, phenoms compare — see the docs.

Outputs default to ./phenom_outputs/ (or $PHENOMS_OUTPUT_DIR).

Benchmarks

Kernel timing (Docker, 4 CPUs, 3×250 frames, 2,722 atoms): Rust 0.047 s vs MDTraj 0.803 s (~17×) vs MDAnalysis 1.126 s (~24×). Reproduce via docker/README.md.

License

MIT

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.2.5)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for Brandon_N from gravatar.com Brandon_N

Credits

Author: Brandon Novy

License

MIT License (MIT)

Requires

Python >=3.8

Provides Extra

benchmark dev docs structure

Tags

molecular-dynamics hydrogen-bonds HDX-MS backbone

Classifiers

Report project as malware

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