Re-packaged with setuptools for standard installation

* 'python setup.py install' will install
  - a package 'propka' (which contains everything that 'Source' contained
    in the original distribution)
  - an executable script 'propka31' (which is identical to the original
    'propka.py' script but it is automatically generated via the setuptools
    mechanism; it uses propka.run.main().
* 'pip install' will also work
* the README.md file was changed to reflect the alterations
* metadata in the setup.py file was added

NOTE: The licence is still unclear!

setup.py

@@ -0,0 +1,51 @@
+# PROPKA 3.1
+#
+#
+# setuptools installation of  PROPKA 3.1
+
+import ez_setup
+ez_setup.use_setuptools()
+from setuptools import setup, find_packages
+
+VERSION = "3.1"
+
+setup(name="PROPKA",
+      version=VERSION,
+      description="Heuristic pKa calculations with ligands",
+      long_description="""
+PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and
+protein-ligand complexes (version 3.1) based on the 3D structure.
+
+For proteins without ligands both version should produce the same result.
+
+The method is described in the following papers, which you should cite
+in publications:
+
+* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan
+  H. Jensen. "Improved Treatment of Ligands and Coupling Effects in
+  Empirical Calculation and Rationalization of pKa Values." Journal of
+  Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
+
+* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan
+  H. Jensen. "PROPKA3: consistent treatment of internal and surface
+  residues in empirical pKa predictions." Journal of Chemical Theory
+  and Computation 7, no. 2 (2011): 525-537.
+
+See http://propka.ki.ku.dk/ for the PROPKA web server,
+using the tutorial http://propka.ki.ku.dk/~luca/wiki/index.php/PROPKA_3.1_Tutorial .
+""",
+      author="Jan H. Jensen",
+      author_email="jhjensen@chem.ku.dk",
+      license="",
+      url="http://propka.ki.ku.dk/",
+      keywords="science",
+      packages=find_packages(exclude=['scripts']),
+      package_data = {'propka': ['*.dat', '*.cfg']},
+      #scripts = ["scripts/propka31.py"],  # use entry point below
+      entry_points = {
+        'console_scripts': [
+            'propka31 = propka.run:main',
+            ],
+        },
+      zip_safe=False,
+)