fixed mild Future Warning (and use reST for README)

README.rst

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+=====================
+  PyQCPROT README
+=====================
+
+* Author:   Joshua L. Adelman, University of Pittsburgh 
+* Contact:  [email protected]
+
+PyQCPROT is a python/cython implementation of Douglas Theobald's `QCP
+method`_ for calculating the minimum RMSD between two structures and
+determining the optimal least-squares rotation matrix.
+
+A full description of the method, along with the original C implementation can 
+be found at http://theobald.brandeis.edu/qcp/
+
+If you use this QCP rotation calculation method in a publication,
+please reference [Theobald2005]_ and [Liu2010]_:
+
+.. [Theobald2005]  Douglas L. Theobald (2005)
+      "Rapid calculation of RMSD using a quaternion-based characteristic polynomial."
+      Acta Crystallographica A 61(4):478-480.
+
+.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)
+      "Fast determination of the optimal rotational matrix for macromolecular superpositions."
+      J. Comput. Chem. 31, 1561-1563. 
+
+
+.. _`QCP method`: http://theobald.brandeis.edu/qcp/
+
+
+License
+======= 
+This code code is released under the BSD 3-clause license as noted in the .pyx source code 
+or LICENSE file. 
+
+The original C code is copyright:
+2009-2010, Pu Liu and Douglas L. Theobald
+
+This implementation is copyright
+2011, Joshua L. Adelman
+
+Installation
+============
+
+This module requires:
+
+- numpy_
+- cython_ (optional)
+- gcc_
+
+.. _numpy: http://numpy.scipy.org/
+.. _cython: http://cython.org/
+.. _gcc: http://gcc.gnu.org/
+
+
+Method 1:
+~~~~~~~~~
+
+To compile the extension in the directory in which ``qcprot.pyx``
+resides::
+
+   python setup.py build_ext --inplace
+
+Further information on `compiling cython extensions`_ is available in 
+the cython_ docs.
+
+.. _`compiling cython extensions`:
+   http://docs.cython.org/src/userguide/source_files_and_compilation.html
+
+
+Method 2
+~~~~~~~~
+
+If you do not have `cython`_ installed, you can build the extension
+directly from the cython generated ``pyqcprot.c``. This is handled
+automatically by ``setup.py``.
+
+
+Example Usage
+=============
+
+See ``example.py`` for a simple example.
+
+For an example using the `MDAnalysis`_ package see
+``mdanalysis_example.py``.
+
+.. _MDAnalysis: https://MDAnalysis.github.io
+