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pyopenms 2.0.1

Python wrapper for C++ LCMS library OpenMS


This package contains Python bindings for a large part of the OpenMS library ( for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).

The pyOpenMS package runs - like OpenMS - on Windows, Linux and OSX.


We provide binary packages for Python 2.7 and 3.3, 3.4 and 3.5 on Windows (64 bit and 32 bit) and Linux 64 bit which makes the installation very straightforward with pip. Note that Python 3.5 is not yet supported under Windows. For other platforms, please refer to the compilation instructions.

Binary installation

On linux machines you can install pyopenms with (you will need numpy in addition):

$ easy_install pyopenms

For other systems first ensure that your pip is up to date, then install the pyopenms wheel (you will need numpy in addition):

$ pip install -U pip
$ pip install -U wheel
$ pip install pyopenms

Source installation

Building the Python packages is generally not straight forward, we recommend that you use the binary packages provided for common Python interpreter versions and operating systems. If you decide to build pyOpenMS on your own, please read and and ask for help on our mailing list


pyOpenMS is published under the 3-clause BSD licence, see ./pyOpenMS/License.txt


pyOpenMS follows the OpenMS documentation very closely. Additionally, there is also a pyOpenMS Manual available. The online manual contains a complete record of every wrapped class and function while the documentation of the corresponding class or function can be inferred from the OpenMS online documentation.

File Type Py Version Uploaded on Size
pyopenms-2.0.1-cp27-cp27m-win32.whl (md5) Python Wheel cp27 2016-09-27 11MB
pyopenms-2.0.1-cp27-cp27m-win_amd64.whl (md5) Python Wheel cp27 2016-09-27 18MB
pyopenms-2.0.1-cp33-cp33m-win32.whl (md5) Python Wheel cp33 2016-09-27 11MB
pyopenms-2.0.1-cp33-cp33m-win_amd64.whl (md5) Python Wheel cp33 2016-09-27 17MB
pyopenms-2.0.1-cp34-cp34m-win32.whl (md5) Python Wheel cp34 2016-09-27 11MB
pyopenms-2.0.1-cp34-cp34m-win_amd64.whl (md5) Python Wheel cp34 2016-09-27 17MB
pyopenms- (md5) Python Egg 2.7 2016-10-01 14MB
pyopenms- (md5) Python Egg 3.4 2016-10-01 13MB
pyopenms- (md5) Python Egg 3.5 2016-10-01 13MB