Metadata-Version: 2.1
Name: efmtool
Version: 0.1.7
Summary: Python wrapper for efmtool.
Home-page: https://gitlab.com/csb.ethz/efmtool
Author: Mattia G. Gollub
Author-email: mattia.gollub@bsse.ethz.ch
License: BSD License
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.
        
        ## Installation
        `pip install efmtool`
        
        ## Usage
        The wrapper provides two ways of calling efmtool:
        1.  Through a simplified interface: 
            
            ```Python
            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](./examples/small_network.py)).
            `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()`.
        
        
        1.  Through a generic wrapper:
            
            ```Python
            efmtool.call_efmtool(
                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](http://doi.org/10.1093/bioinformatics/btn401)
        
        
        ## Credits
        efmtool is a software written by Marco Terzer (ETH Zurich).
        
        Python wrapper by Mattia Gollub (ETH Zurich).
Keywords: EFM,EFMs,Elementary Flux Modes,efmtool,metabolic network,reaction network
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
