Euclid
=======


Installation:
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To use EuclidComputeDrifts, there are a few dependencies.
They should all install with just `python setup.py install`


(0) MSMBuilder Extras

    To compute the drift in dihedrals, we use code from 
    msmbuilder/Extras/Geometry. Make sure the Extras directory is included
    in your PYTHONPATH. To check if the Geometry module is available, in an 
    ipython session, try

    >> from Geometry import DihedralTools

    Note that you need to be using at the msmbuilder development branch,
    at least revision 613.

(1) deap - Distributed Evolutionary Algorithms in Python.

    Specifically, we use the dtm module that they have, which is a distributed 
    task manager capable of spreading the workload over multiple cores/nodes 
    via mpi (using mpi4py).

    deap is available by on pypi, which means that you can install it with 
    easy_install or pip

    $ pip install deap
    or 
    $ easy_install deap




Using EuclidComputeDrifts:
=====
EuclidComputeDrifts uses a YAML input file. See ComputeDrift_example_input.yaml
(it's just plain text) for a description of all the options.