pyopenms

library3.5.0pypypi✓ verified 89d ago

pyOpenMS is the Python wrapper for OpenMS, a C++ library for LC-MS data analysis and computational proteomics. Current version 3.5.0. Release cadence is approximately bi-annual.

ai-ml data

pip install pyopenms

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · PYOPENMS

pyopenms

ai-mlpythonv3.5.0

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

MSExperiment

✓ from pyopenms import MSExperiment

MZMLFile

✓ from pyopenms import MZMLFile

Load an mzML file and count MS2 spectra.

from pyopenms import MSExperiment, MZMLFile exp = MSExperiment() MZMLFile().load("input.mzML", exp) print(f"Number of spectra: {exp.size()}") ms2 = [s for s in exp if s.getMSLevel() == 2] print(f"Number of MS2 spectra: {len(ms2)}")

Debug

Known issues

gotchaLibrary is large and can take a long time to install or import; first import may appear to hang.

fix

Be patient; pre-built wheels are available on PyPI for many platforms. Use a virtual environment.

affects: all

gotchaSome functions accept C++ types directly; passing Python lists of strings may fail silently or raise cryptic errors.

fix

Use pyopenms types like StringList or std::vector wrappers when expected.

affects: all

Errors

Common errors & fixes

ImportError: No module named pyopenms

Library not installed or installed in wrong environment.

fix

Run `pip install pyopenms` in your active Python environment. Ensure you are using Python 3.7+.

OSError: libOpenMS.so: cannot open shared object file

Missing OpenMS C++ runtime libraries (on Linux/macOS).

fix

Install pyopenms via conda: `conda install -c conda-forge pyopenms`. This resolves shared library dependencies.

Upgrade

Version history

3.5.0latest on PyPI · released Dec 11, 2025

Audit

Dependencies

numpyrequiredRequired for numerical operations

matplotliboptionalOptional for plotting spectra

Agent activity

18 hits · last 30 days

node

Anthropic

OpenAI (training)

Resources

githubhttps://github.com/OpenMS/pyopenms-docs ↗

packagehttps://pypi.org/project/pyopenms/ ↗

homepagehttps://openms.de ↗

docshttps://pyopenms.readthedocs.io ↗