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
1 maintainer
Metadata
1 maintainer
Release files for phenoms 0.2.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| phenoms-0.2.6.tar.gz | 2.4 MB | Details |
Built distributions (wheels)
Total release size: 9.0 MB
Release files / phenoms-0.2.6.tar.gz
| Download URL | phenoms-0.2.6.tar.gz |
|---|---|
| Size | 2.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
9f878336a79d45ca363bd8363e9397c737a5fe1da5d823992eaa54f9ce464760
|
|
BLAKE2b-256 checksum How to use checksums |
37d2156cea139135d72396b0440fffa1e2dc56adfccfadbdd0012e03f62f6ff1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp313-cp313-win_amd64.whl
| Download URL | phenoms-0.2.6-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 248.5 kB |
| Tags | CPython 3.13 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
1e5438ec6175858e1285fbd22c51156951655f83482b07d43c380a08e7f12f1b
|
|
BLAKE2b-256 checksum How to use checksums |
f79cd89f498c7fbb1b8812f551a5de8d2ab145c420a3eb5e298ac97218ace30b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | phenoms-0.2.6-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 420.5 kB |
| Tags | CPython 3.13 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
0162e9a5a38688e452689045e958a47d2e991a6d8ddea0caddbc65645597d1de
|
|
BLAKE2b-256 checksum How to use checksums |
077d262bd4811426545a843baf68c227d793c1bf09feda26d7ebcca4c3038eef
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp313-cp313-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | phenoms-0.2.6-cp313-cp313-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 664.6 kB |
| Tags | CPython 3.13 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
875be7304bc040c84ce6f5f234d6e5a13e3c0b955fc8eb56920559ae81359233
|
|
BLAKE2b-256 checksum How to use checksums |
ea2cfe31c55adf13aca289b31d0488879947600fa0a7f2e1e8c75b1e47b85fc8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp312-cp312-win_amd64.whl
| Download URL | phenoms-0.2.6-cp312-cp312-win_amd64.whl |
|---|---|
| Size | 248.6 kB |
| Tags | CPython 3.12 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
377ca29970714e3d27eb32cd9958f6d088589580450c6306041acb85452ad346
|
|
BLAKE2b-256 checksum How to use checksums |
5deccaf1ae63154c6b154dd71408e5cc58f291d5df80086cd98712bbb75b749b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | phenoms-0.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 420.8 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
3510e1f29c81a9af88b9d4ac59fe0e65c70461d1083dc60bd69f4850009ffa6a
|
|
BLAKE2b-256 checksum How to use checksums |
518bdee9f4d19066aae97e8a4d1ab86904e48e20c3d30d2965529b90c589efa9
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp312-cp312-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | phenoms-0.2.6-cp312-cp312-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 664.9 kB |
| Tags | CPython 3.12 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
1be9c43581c89611d126d097c09bfc860f397eee2a426cbb18b88c0cf78baf43
|
|
BLAKE2b-256 checksum How to use checksums |
a14d4fab58daf35d8b52decbba073afad7c4c9ff60b89f93e387eebfc8f32206
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp311-cp311-win_amd64.whl
| Download URL | phenoms-0.2.6-cp311-cp311-win_amd64.whl |
|---|---|
| Size | 248.8 kB |
| Tags | CPython 3.11 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
1405b443955b015e742af44ce1769d4850fb11c4b7236f1bf9d4095e88bed5cd
|
|
BLAKE2b-256 checksum How to use checksums |
ef178da99230da1728daaa93c1f22f76d794a3b051a7c916536175f02804f6d5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | phenoms-0.2.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 419.9 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
0306c9209eb27eb8529e463bfe66be524990438dcb493d083ef3591afc881a23
|
|
BLAKE2b-256 checksum How to use checksums |
a6251fd37b6e08681d21946a575962a156cc765a2b6dd2601b3aaefdfdf10c70
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp311-cp311-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | phenoms-0.2.6-cp311-cp311-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 664.5 kB |
| Tags | CPython 3.11 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
3cc5288ac7dc0bead180b228b56acf7ef7a573d5c9b10ea5c4d2bc7eb65b7432
|
|
BLAKE2b-256 checksum How to use checksums |
13d93637dc03c429c2eb2b4292364078ee311f04f95f44b0fb4107e87d27e75e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp310-cp310-win_amd64.whl
| Download URL | phenoms-0.2.6-cp310-cp310-win_amd64.whl |
|---|---|
| Size | 249.4 kB |
| Tags | CPython 3.10 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
bc81cb4df79cac675a3bbbadca5503b70e9b1d7293681bcc3c48438bbb1a5f59
|
|
BLAKE2b-256 checksum How to use checksums |
ece6a365ca13f07437ef72c9fc50ea0e8e3f53ff2387653106ab20caeea101d3
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | phenoms-0.2.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 419.5 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
b4b34c35ee52d0be8a3857f68678b4d5009c3f536f620b3de0578fb0ebbb2efb
|
|
BLAKE2b-256 checksum How to use checksums |
dfe6744fac0bb85c25594a4aae746b0ef10ede9036fec0743cfcfa7c8846788f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp310-cp310-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | phenoms-0.2.6-cp310-cp310-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 664.5 kB |
| Tags | CPython 3.10 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
82b8ae9ded271d38d37ed200dc98ef94f4864f75884fe94e0966f2f976efe367
|
|
BLAKE2b-256 checksum How to use checksums |
078f4746979709cc40ea09f92ecb1d50cbf904ae0c06db5fa986174bec35d746
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp39-cp39-win_amd64.whl
| Download URL | phenoms-0.2.6-cp39-cp39-win_amd64.whl |
|---|---|
| Size | 250.3 kB |
| Tags | CPython 3.9 Windows x86-64 |
|
SHA-256 checksum How to use checksums |
1bf82e350e5f556e1538bf5594a90181e4d8664a038ef7d14a9e36f03d65acf7
|
|
BLAKE2b-256 checksum How to use checksums |
7343714ef515b0c0269c87cd9a2d6f3805f3be954a1308accd852599ae5808d2
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | phenoms-0.2.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 420.0 kB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
2075652b876199b96ad2107ddaa91bae53546414aee9d2d5643b9d136fc4b4e6
|
|
BLAKE2b-256 checksum How to use checksums |
0cca56c5f1b4911cc5cacac7c424d55314ad09bd9ac8c68dc29dbe27f64c4a37
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency logRelease files / phenoms-0.2.6-cp39-cp39-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | phenoms-0.2.6-cp39-cp39-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 667.3 kB |
| Tags | CPython 3.9 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
b6a3f9a6da8ed8954e9c9797a0476a04eecf1bf789301671e4703f820e8e892d
|
|
BLAKE2b-256 checksum How to use checksums |
5adf9a7eda969242bf96f137c7f07dcfb76d857c86256c75c2034ce95b69b4ae
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 7, 2026.
Transparency log
