LPRMSD : Linear Programming RMSD Distance Metric for MSMBuilder
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Overview
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Modified version of RMSD distance metric that does the following

1) Returns the RMSD, rotation matrices, and aligned conformations
2) Permutes selected atomic indices.
3) Perform the alignment again.

Installation
------------
Run `python setup.py install`. LPRMSD links to BLAS, so you need to have blas
on your system. If you have BLAS installed in a nonstandard location, you can
provide the path to it in setup.cfg

On ubuntu, you can install blas via `sudo apt-get install libblas-dev`.

Usage
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After installing, you will see `lprmsd` as a choice in MSMBuilder scripts which
require a distance metric, such as `Cluster.py`