Skip to main content

Python wrapper for efmtool.

Project description

Python wrapper for efmtool

efmtool is a Java software for the enumeration of Elementary Flux Modes (EFMs) developed by Marco Terzer at ETH Zurich. This package provides a simple Python wrapper.


pip install efmtool


The wrapper provides two ways of calling efmtool:

  1. Through a simplified interface:

    efms = efmtool.calculate_efms(
        stoichiometry : np.array,
        reversibilities : List[int],
        reaction_names : List[str],
        metabolite_names : List[str],
        options : Dict = None,
        jvm_options : List[str] = None)

    This function directly returns a NumPy array containing all the EFMs of the specified network (example). reversibilities is a list indicating whether a reaction is reversible (1) or not (0). Note that irreversibilities are assumed to be in forward directions. If a reaction is irreversible in the backward direction, it should be reversed before calling efmtool. Default options can be obtained through get_default_options().

  2. Through a generic wrapper:

        args : List[str],
        jvm_options : List[str] = None)

    The wrapper simply calls efmtool passing the specified arguments. Specifying, writing and reading input/output temporary files is responsibility of the user.

See config/metabolic-efm.xml, the documentation, or run java -cp lib/metabolic-efm-all.jar ch.javasoft.metabolic.efm.main.CalculateFluxModes --help for more information about the available options.

Cite us

If you use efmtool in a scientific publication, please cite our paper:

Terzer, M., Stelling, J., 2008. "Large-​scale computation of elementary flux modes with bit pattern trees". Bioinformatics. - link


efmtool is a software written by Marco Terzer (ETH Zurich).

Python wrapper by Mattia Gollub (ETH Zurich).

Thanks to Axel Theorell (ETH Zurich) for OSX compatibility fixes.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

efmtool-0.2.0.tar.gz (5.6 MB view hashes)

Uploaded source

Built Distribution

efmtool-0.2.0-py2.py3-none-any.whl (5.6 MB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page