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

pip install phenoms

Reading GROMACS .tpr topologies needs one optional extra:

pip install "phenoms[gromacs]"

Every other supported format (.gro/.pdb topologies, OpenMM .dcd, AMBER .nc/.prmtop, multi-frame PDBs) works with the plain install above — see the Inputs docs for the full file-type breakdown.

Quick start

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

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 gromacs

Tags

molecular-dynamics hydrogen-bonds HDX-MS backbone

Classifiers

Report project as malware

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