============ Installation ============ Obtaining the code ------------------ If you have `Mercurial`_ installed, you can clone the repository using:: $ hg clone https://bitbucket.org/joshua.adelman/stringmethodexamples Alternatively, you can download a compressed archive of the code by going to https://bitbucket.org/joshua.adelman/stringmethodexamples/downloads and selecting the ``Branches`` tab and selecting one of the archive formats for the ``default`` branch. Dependencies ------------ This code makes use of a number of freely available third-party libraries. You must first install WESTPA (http://chong.chem.pitt.edu/WESTPA) and all of its dependencies. This package also makes use of several additional libraries for analyzing data generated by the simulations: * `bottleneck`_ * `pymbar`_ It is generally recommended to use either the `Enthought Python Distribution`_ (Academic) or the `Anaconda`_ distribution (CE or Pro) to install all of the basic dependencies. Then install `bottleneck`_ and `pymbar`_ either into that version of python or into a separate directory that is on the ``PYTHONPATH``. The code assumes that the dependencies are available through the python executable returned by ``which python``, and that you are using a bash based shell on a Unix system (both Linux and OS X should work). Setup ----- A Makefile is provided to build all of the python extension included in the package and setup the run scripts, environmental variables and symbolic links. First set ``$WEST_ROOT`` to the directory containing the `WESTPA`_ package:: $ export WEST_ROOT= and then run make:: $ cd stringmethodexamples $ make .. DEPENDENCIES LINKS .. _`WESTPA`: http://chong.chem.pitt.edu/WESTPA .. _`bottleneck`: http://berkeleyanalytics.com/bottleneck/ .. _`pymbar`: https://simtk.org/home/pymbar .. _`Enthought Python Distribution`: http://www.enthought.com/products/epd.php .. _`Anaconda`: https://store.continuum.io/cshop/anaconda .. _`Mercurial`: http://mercurial.selenic.com/