Metadata-Version: 1.2
Name: scipion-em-eman2
Version: 3.1.1
Summary: Plugin to use EMAN2 programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-eman2
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-eman2/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-eman2/
Description: ============
        EMAN2 plugin
        ============
        
        This plugin provide wrappers around several programs of `EMAN2 <https://blake.bcm.edu/emanwiki/EMAN2>`_ software suite.
        
        +------------------+------------------+
        | stable: |stable| | devel: | |devel| |
        +------------------+------------------+
        
        .. |stable| image:: http://scipion-test.cnb.csic.es:9980/badges/eman2_prod.svg
        .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/eman2_sdevel.svg
        
        
        Installation
        ------------
        
        You will need to use `3.0 <https://github.com/I2PC/scipion/releases/tag/V3.0.0>`_ 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-eman2
        
        b) Developer's version
        
            * download repository
        
            .. code-block::
        
                git clone https://github.com/scipion-em/scipion-em-eman2.git
        
            * install
        
            .. code-block::
        
                scipion installp -p path_to_scipion-em-eman2 --devel
        
        EMAN2 binaries will be installed automatically with the plugin, but you can also link an existing installation.
        
            * Default installation path assumed is ``software/em/eman-2.31``, if you want to change it, set *EMAN2_HOME* in ``scipion.conf`` file pointing to the folder where the EMAN2 is installed.
        
            **IMPORTANT: From plugin version 1.0.5 EMAN2DIR was renamed to EMAN2_HOME. Please update your scipion.conf file!**
        
            * If you need to pass special options to mpirun (like a hostfile), you can use the *EMANMPIOPTS* shell variable, but most users should not need this. A typical usage would be ``export EMANMPIOPTS="-hostfile myhosts.txt"``. You should only do this if necessary, though (note that then when supplying the parameter **--parallel=mpi:n:scratch_directory**, 'n' is no longer the number of cpus to use, but rather the number of nodes listed in myhosts.txt).
            * The default scratch directory is assumed */tmp/*. You can change it by setting *EMAN2SCRATCHDIR* in your shell environment.
        
        To check the installation, simply run one of the following Scipion tests:
        
        .. code-block::
        
           scipion test eman2.tests.test_protocols_eman.TestEmanTiltValidate
           scipion test eman2.tests.test_protocols_eman.TestEmanRefineEasy
           scipion test eman2.tests.test_protocols_eman.TestEmanRefine2DBispec
           scipion test eman2.tests.test_protocols_eman.TestEmanRefine2D
           scipion test eman2.tests.test_protocols_eman.TestEmanReconstruct
           scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelMda
           scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelGroel
           scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelSGD
           scipion test eman2.tests.test_protocols_eman.TestEmanCtfAuto
           scipion test eman2.tests.test_protocols_eman.TestEmanAutopick
        
        A complete list of tests can also be seen by executing ``scipion test --show --grep eman``
        
        Supported versions
        ------------------
        
        2.3, 2.31
        
        In 2018 the plugin was updated to support the latest (at that moment) EMAN2: 2.21. This required a lot of code refactoring and the support of old EMAN2 version 2.11 had to be discontinued. Several new protocols were added: 2D refinements, tilt validation, ctf-auto and new e2boxer. The full changelog since Scipion-1.x is available `here <https://github.com/scipion-em/scipion-em-eman2/issues/1>`_.
        
        Protocols
        ---------
        
        * `boxer (old and new interactive e2boxer.py) <https://github.com/scipion-em/scipion-em-eman2/wiki/EmanProtBoxing>`_
        * boxer auto (fully automated new boxer in >=2.21)
        * ctf auto
        * `initial model <https://github.com/scipion-em/scipion-em-eman2/wiki/EmanProtInitModel>`_
        * initial model SGD
        * reconstruct
        * refine 2d
        * refine 2d bispec
        * refine easy
        * `sparx picker <https://github.com/scipion-em/scipion-em-eman2/wiki/SparxGaussianProtPicking>`_
        * tilt validate
        
        References
        ----------
        
        1. \G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
