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        "description": "rms2dfinder\n===============\n.. image:: https://pypip.in/py_versions/rms2dfinder/badge.svg\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Supported Python versions\n\n.. image:: https://pypip.in/status/rms2dfinder/badge.svg\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Development Status\n.. image:: https://pypip.in/d/rms2dfinder/badge.png\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Downloads\n\n.. image:: https://pypip.in/v/rms2dfinder/badge.png\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Latest version\n\n.. image:: https://pypip.in/wheel/rms2dfinder/badge.png\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Wheel Status\n\n.. image:: https://pypip.in/egg/rms2dfinder/badge.png\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: Egg Status\n\n.. image:: https://pypip.in/license/rms2dfinder/badge.png\n    :target: https://pypi.python.org/pypi/rms2dfinder/\n    :alt: License\n\n.. image:: https://requires.io/github/lambdalisue/rms2dfinder/requirements.svg?branch=master\n    :target: https://requires.io/github/lambdalisue/rms2dfinder/requirements/?branch=master\n    :alt: Requirements Status\n\n.. image:: https://landscape.io/github/lambdalisue/rms2dfinder/master/landscape.png\n    :target: https://landscape.io/github/lambdalisue/rms2dfinder/master\n    :alt: Code Health\n\n\n``rms2d`` command in ``cpptraj`` of Amber is quite useful to find several structural clusters.\nYou can visually classify the trajectories into several clusters of structures and can find out a most stable structure in each cluster by finding out the frame which has a smallest value of total RMSd in each cluster.\nHowever, it is a tough job to find out **exact** frame number which has a smallest value.\n\n``rms2dfinder`` will help you to find the frame numbers which have minimum mean RMSd in each cluster. What you need to do is just select the region on rms2d plot and the software tells you\n\n-   A minimum mean RMSd (Mean value of summed up RMSd in the region)\n-   A frame number which has the minimum mean RMSd\n-   Start and end frame number\n\nSee the screenshot below\n\n.. image:: res/screenshot001.png\n\n\nInstall\n-------------\n\nUse `pip <https://pypi.python.org/pypi/pip>`_ to install as:\n\n    pip install rms2dfinder\n\n\nRequirements\n-------------\n\nIt require `Python <https://www.python.org/>`_ and following python libraries\n\n-   `numpy <http://www.numpy.org/>`_\n-   `matplotlib <http://matplotlib.org/>`_\n\nAll libraries are automatically installed if you install ``rms2dfinder`` via ``pip``.\n\n\nUsage\n------------\n\n    usage: rms2dfinder.py [-h] infile\n\n    A helper utility to find minimum mean RMSd structures of clusters found in\n    rms2d plot.\n\n    positional arguments:\n    infile      A file generated by rms2d command in cpptraj of Amber.\n\n    optional arguments:\n    -h, --help  show this help message and exit\n\n\nLicense\n--------\nThe MIT License (MIT)\n\nCopyright (C) 2014 hashnote.net, Alisue\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.",
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