=============
Cryoef plugin
=============
This plugin provides a wrapper for `cryoEF <https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF/>`_ program.
.. image:: https://img.shields.io/pypi/v/scipion-em-cryoef.svg
:target: https://pypi.python.org/pypi/scipion-em-cryoef
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-cryoef.svg
:target: https://pypi.python.org/pypi/scipion-em-cryoef
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-cryoef.svg
:target: https://pypi.python.org/pypi/scipion-em-cryoef
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-cryoef?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-cryoef
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-cryoef
:target: https://pypi.python.org/pypi/scipion-em-cryoef
: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-cryoef
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-cryoef.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-cryoef --devel
CryoEF binaries will be installed automatically with the plugin, but you can also link an existing installation.
Default installation path assumed is ``software/em/cryoEF-1.1.0``, if you want to change it, set *CRYOEF_HOME* in `scipion.conf`` file to the folder where the cryoEF is installed. To check the installation, simply run the following Scipion test:
``scipion test cryoef.tests.test_protocols_cryoef.TestCryoEF``
Supported versions
------------------
1.1.0
Protocols
---------
* orientation analysis
Detailed manual can be found in ``software/em/cryoEF-1.1.0/cryoEF_v1.1.0_manual.pdf``
References
----------
* `1. Naydenova, K and Russo, CJ "Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy" Nature Communications (2017). <https://www.nature.com/articles/s41467-017-00782-3>`_
Raw data
{
"_id": null,
"home_page": "https://github.com/scipion-em/scipion-em-cryoef",
"name": "scipion-em-cryoef",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0",
"author": "Grigory Sharov",
"author_email": "sharov.grigory@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/4a/98/6e5eae982cabced4b035b4b07f7dc38b8c138b0be308d922eec3d3bcc62e/scipion-em-cryoef-3.0.15.tar.gz",
"platform": null,
"description": "=============\nCryoef plugin\n=============\n\nThis plugin provides a wrapper for `cryoEF <https://www.mrc-lmb.cam.ac.uk/crusso/cryoEF/>`_ program.\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-cryoef.svg\n :target: https://pypi.python.org/pypi/scipion-em-cryoef\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-cryoef.svg\n :target: https://pypi.python.org/pypi/scipion-em-cryoef\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-cryoef.svg\n :target: https://pypi.python.org/pypi/scipion-em-cryoef\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-cryoef?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-cryoef\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-cryoef\n :target: https://pypi.python.org/pypi/scipion-em-cryoef\n :alt: Downloads\n\nInstallation\n------------\n\nYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-cryoef\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-cryoef.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-cryoef --devel\n\nCryoEF binaries will be installed automatically with the plugin, but you can also link an existing installation. \nDefault installation path assumed is ``software/em/cryoEF-1.1.0``, if you want to change it, set *CRYOEF_HOME* in `scipion.conf`` file to the folder where the cryoEF is installed. To check the installation, simply run the following Scipion test:\n\n``scipion test cryoef.tests.test_protocols_cryoef.TestCryoEF``\n\nSupported versions\n------------------\n\n1.1.0\n\nProtocols\n---------\n\n * orientation analysis\n\nDetailed manual can be found in ``software/em/cryoEF-1.1.0/cryoEF_v1.1.0_manual.pdf``\n\nReferences\n----------\n\n * `1. Naydenova, K and Russo, CJ \"Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy\" Nature Communications (2017). <https://www.nature.com/articles/s41467-017-00782-3>`_\n\n\n",
"bugtrack_url": null,
"license": "",
"summary": "Plugin to use Cryoef program within the Scipion framework",
"version": "3.0.15",
"project_urls": {
"Bug Reports": "https://github.com/scipion-em/scipion-em-cryoef/issues",
"Homepage": "https://github.com/scipion-em/scipion-em-cryoef",
"Source": "https://github.com/scipion-em/scipion-em-cryoef/"
},
"split_keywords": [
"scipion",
"electron-microscopy",
"cryo-em",
"structural-biology",
"image-processing",
"scipion-3.0"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "cd5506ecf5a7d3367529501cad107bafedaff04aa6ba9ba6e7c8fdfec7bda9a4",
"md5": "39d1e71d29342927f567b2ff9109c529",
"sha256": "1d29606eb97f5a98f076d87fcc3fbe563dac778186d493cd24994dc9a9b37e9d"
},
"downloads": -1,
"filename": "scipion_em_cryoef-3.0.15-py3-none-any.whl",
"has_sig": false,
"md5_digest": "39d1e71d29342927f567b2ff9109c529",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 30156,
"upload_time": "2023-11-19T13:49:57",
"upload_time_iso_8601": "2023-11-19T13:49:57.394045Z",
"url": "https://files.pythonhosted.org/packages/cd/55/06ecf5a7d3367529501cad107bafedaff04aa6ba9ba6e7c8fdfec7bda9a4/scipion_em_cryoef-3.0.15-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "4a986e5eae982cabced4b035b4b07f7dc38b8c138b0be308d922eec3d3bcc62e",
"md5": "9ed793c7effff46714c9513183e5fd42",
"sha256": "8286d94b7b32da723be7e423bf1c6c3e2f1a5eabb6d51a09996a2757c60d4947"
},
"downloads": -1,
"filename": "scipion-em-cryoef-3.0.15.tar.gz",
"has_sig": false,
"md5_digest": "9ed793c7effff46714c9513183e5fd42",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 26673,
"upload_time": "2023-11-19T13:49:59",
"upload_time_iso_8601": "2023-11-19T13:49:59.216893Z",
"url": "https://files.pythonhosted.org/packages/4a/98/6e5eae982cabced4b035b4b07f7dc38b8c138b0be308d922eec3d3bcc62e/scipion-em-cryoef-3.0.15.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-19 13:49:59",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-em-cryoef",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "scipion-em-cryoef"
}
JSON
