rms2dfinder
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
Install
Use pip to install as:
pip install rms2dfinder
Requirements
It require Python and following python libraries
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.
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Metadata
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Release files for rms2dfinder 0.1.2
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