rms2dfinder 0.1.2
A helper utility to find minimum mean RMSd structures of clusters found in rms2d plot.
License: MIT
Keywords: utility Amber rms2d molecular dynamics

rms2dfinder
===============
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``rms2d`` command in ``cpptraj`` of Amber is quite useful to find several structural clusters.
You 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.
However, it is a tough job to find out **exact** frame number which has a smallest value.

``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

-   A minimum mean RMSd (Mean value of summed up RMSd in the region)
-   A frame number which has the minimum mean RMSd
-   Start and end frame number

See the screenshot below

.. image:: res/screenshot001.png


Install
-------------

Use `pip <https://pypi.python.org/pypi/pip>`_ to install as:

    pip install rms2dfinder


Requirements
-------------

It require `Python <https://www.python.org/>`_ and following python libraries

-   `numpy <http://www.numpy.org/>`_
-   `matplotlib <http://matplotlib.org/>`_

All libraries are automatically installed if you install ``rms2dfinder`` via ``pip``.


Usage
------------

    usage: rms2dfinder.py [-h] infile

    A helper utility to find minimum mean RMSd structures of clusters found in
    rms2d plot.

    positional arguments:
    infile      A file generated by rms2d command in cpptraj of Amber.

    optional arguments:
    -h, --help  show this help message and exit


License
--------
The MIT License (MIT)

Copyright (C) 2014 hashnote.net, Alisue

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.