===============
OPUS-DSD plugin
===============
This plugin provides a wrapper for `OPUS-DSD <https://github.com/alncat/opusDSD>`_ software: Deep structural disentanglement for cryo-EM single-particle analysis.
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-opusdsd
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-opusdsd.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-opusdsd --devel
OPUS-DSD software will be installed automatically with the plugin but you can also use an existing installation by providing *OPUSDSD_ENV_ACTIVATION* (see below).
**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
Configuration variables
-----------------------
*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the
PATH (not recommended), which can lead to execution problems mixing scipion
python with conda ones. One example of this could can be seen below but
depending on your conda version and shell you will need something different:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
*OPUSDSD_ENV_ACTIVATION* (default = conda activate opusdsd-2.3.0):
Command to activate the opusdsd environment.
Verifying
---------
To check the installation, simply run the following Scipion test:
``scipion test opusdsd.tests.test_protocols_opusdsd.TestOpusDsd``
Supported versions
------------------
0.3.2b
v1.1.0
Protocols
----------
* training CV/Multi
* analyze/eval_vol (volume generation)
References
-----------
1. OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Zhenwei Luo, Fengyun Ni, Qinghua Wang, Jianpeng Ma. https://www.nature.com/articles/s41592-023-02031-6
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"description": "===============\nOPUS-DSD plugin\n===============\n\nThis plugin provides a wrapper for `OPUS-DSD <https://github.com/alncat/opusDSD>`_ software: Deep structural disentanglement for cryo-EM single-particle analysis.\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-opusdsd\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-opusdsd.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-opusdsd --devel\n\nOPUS-DSD software will be installed automatically with the plugin but you can also use an existing installation by providing *OPUSDSD_ENV_ACTIVATION* (see below).\n\n**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.\n\nConfiguration variables\n-----------------------\n*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the\nPATH (not recommended), which can lead to execution problems mixing scipion\npython with conda ones. One example of this could can be seen below but\ndepending on your conda version and shell you will need something different:\nCONDA_ACTIVATION_CMD = eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"\n\n*OPUSDSD_ENV_ACTIVATION* (default = conda activate opusdsd-2.3.0):\nCommand to activate the opusdsd environment.\n\n\nVerifying\n---------\nTo check the installation, simply run the following Scipion test:\n\n``scipion test opusdsd.tests.test_protocols_opusdsd.TestOpusDsd``\n\nSupported versions\n------------------\n\n0.3.2b\n\nv1.1.0\n\nProtocols\n----------\n\n* training CV/Multi\n* analyze/eval_vol (volume generation)\n\nReferences\n-----------\n\n1. OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Zhenwei Luo, Fengyun Ni, Qinghua Wang, Jianpeng Ma. https://www.nature.com/articles/s41592-023-02031-6\n",
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