Metadata-Version: 1.2
Name: scipion-em-cistem
Version: 3.4
Summary: Plugin to use cisTEM programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-cistem
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-cistem/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-cistem/
Description: =============
        cisTEM plugin
        =============
        
        This plugin provides wrappers for several programs of `cisTEM <https://cistem.org>`_ software suite.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-cistem.svg
                :target: https://pypi.python.org/pypi/scipion-em-cistem
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-cistem.svg
                :target: https://pypi.python.org/pypi/scipion-em-cistem
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-cistem.svg
                :target: https://pypi.python.org/pypi/scipion-em-cistem
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-cistem?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-cistem
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-cistem
                :target: https://pypi.python.org/pypi/scipion-em-cistem
                :alt: Downloads
        
        Installation
        ------------
        
        You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
        
        a) Stable version
        
        .. code-block::
        
            scipion installp -p scipion-em-cistem
        
        b) Developer's version
        
            * download repository
        
            .. code-block::
        
                git clone -b devel https://github.com/scipion-em/scipion-em-cistem.git
        
            * install
        
            .. code-block::
        
                scipion installp -p /path/to/scipion-em-cistem --devel
        
        cisTEM binaries will be installed automatically with the plugin, but you can also link an existing installation.
        
            * Default installation path assumed is ``software/em/cistem-1.0.0-beta``, if you want to change it, set *CISTEM_HOME* in ``scipion.conf`` file pointing to the folder where the cisTEM is installed.
            * It's possible to use CTFFIND4 installed separately from cisTEM by defining *CTFFIND4_HOME* variable in ``scipion.conf``. Setting this value will have the priority over Ctffind inside cisTEM.
        
        A complete list of tests can be seen by executing ``scipion test --show --grep cistem``
        
        Supported versions
        ------------------
        
        * 1.0.0-beta (cistem)
        * 4.1.13, 4.1.14 (ctffind4)
        
        Protocols
        ---------
        
        * ctffind4
        * import tomo CTFs
        * tilt-series ctffind4
        * unblur
        * find particles
        * classify 2D
        
        References
        ----------
        
        1. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
