This release is a pre-release and may not be stable for production use.
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://popov-lab-unc.github.io/PHENOMS/ Source: https://github.com/Brandon-Cole/PHENOMS
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for phenoms 0.2.7a1
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