========================================
Kihara Lab plugin
========================================
This is a **Scipion** plugin that offers different `Kihara Lab tools <https://kiharalab.org/>`_.
These tools will make it possible to carry out different functions for working with electron density maps.
The code involving these functionalities can be found at https://github.com/kiharalab.
Therefore, this plugin allows to use programs from the DAQ software suite
within the Scipion framework.
========================================
Install this plugin
========================================
You will need to use `Scipion3 <https://scipion-em.github.io/docs/docs/scipion
-modes/how-to-install.html>`_ to run these protocols.
DAQ, Emap2sec, Emap2sec+, and MainMast are installed automatically by scipion.
**Note:** Emap2sec+ needs an Nvidia GPU to run.
- **Install the stable version**
Through the plugin manager GUI by launching Scipion and following **Others** >> **Plugin Manager**
or
.. code-block::
scipion3 installp -p scipion-em-kiharalab
- **Developer's version**
1. Download repository:
.. code-block::
git clone https://github.com/scipion-em/scipion-em-kiharalab.git
2. Install:
.. code-block::
scipion3 installp -p path_to_scipion-em-kiharalab --devel
========================================
Protocols
========================================
scipion-em-kiharalab contains the following protocols:
- **DAQ model validation**: Executes the DAQ software to validate a structure model
- **Emap2sec**: Identifies protein secondary structures
- **segment map**: performs the segmentation of maps into different regions by using mainmast software
========================================
Packages & enviroments
========================================
Packages installed by this plugin can be located in ``/path/to/scipion/software/em/``.
The following packages will be created:
- daq-``version``
- emap2sec-``version``
- mainMast-``version``
Where ``version`` is the current version of that specific package.
Also, the following conda enviroments will be created:
- daq-``version``
- emap2sec-``version``
- emap2secPlus-``version``
As of today, Scipion does not automatically uninstall the conda enviroments created in the installation process when uninstalling a plugin, so keep this list in mind if you want to clean up some disk space if you need to uninstall scipion-em-kiharalab.
========================================
Changelog
========================================
All the recent version changes can be found `here <https://github.com/scipion-em/scipion-em-kiharalab/blob/devel/CHANGES.rst>`_.
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"description": "========================================\nKihara Lab plugin\n========================================\nThis is a **Scipion** plugin that offers different `Kihara Lab tools <https://kiharalab.org/>`_.\nThese tools will make it possible to carry out different functions for working with electron density maps.\nThe code involving these functionalities can be found at https://github.com/kiharalab.\n\nTherefore, this plugin allows to use programs from the DAQ software suite\nwithin the Scipion framework.\n\n========================================\nInstall this plugin\n========================================\nYou will need to use `Scipion3 <https://scipion-em.github.io/docs/docs/scipion\n-modes/how-to-install.html>`_ to run these protocols.\n\nDAQ, Emap2sec, Emap2sec+, and MainMast are installed automatically by scipion.\n\n**Note:** Emap2sec+ needs an Nvidia GPU to run.\n\n- **Install the stable version**\n\n Through the plugin manager GUI by launching Scipion and following **Others** >> **Plugin Manager**\n\n or\n\n.. code-block::\n\n scipion3 installp -p scipion-em-kiharalab\n\n\n- **Developer's version**\n\n 1. Download repository:\n\n .. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-kiharalab.git\n\n 2. Install:\n\n .. code-block::\n\n scipion3 installp -p path_to_scipion-em-kiharalab --devel\n\n========================================\nProtocols\n========================================\nscipion-em-kiharalab contains the following protocols:\n\n- **DAQ model validation**: Executes the DAQ software to validate a structure model\n- **Emap2sec**: Identifies protein secondary structures\n- **segment map**: performs the segmentation of maps into different regions by using mainmast software\n\n========================================\nPackages & enviroments\n========================================\nPackages installed by this plugin can be located in ``/path/to/scipion/software/em/``.\n\nThe following packages will be created:\n\n- daq-``version``\n- emap2sec-``version``\n- mainMast-``version``\n\nWhere ``version`` is the current version of that specific package.\n\nAlso, the following conda enviroments will be created:\n\n- daq-``version``\n- emap2sec-``version``\n- emap2secPlus-``version``\n\nAs of today, Scipion does not automatically uninstall the conda enviroments created in the installation process when uninstalling a plugin, so keep this list in mind if you want to clean up some disk space if you need to uninstall scipion-em-kiharalab.\n\n========================================\nChangelog\n========================================\nAll the recent version changes can be found `here <https://github.com/scipion-em/scipion-em-kiharalab/blob/devel/CHANGES.rst>`_.\n",
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