adjusted test script: all tests pass

* renamed scripts/propka.py to propka31.py so that it can be run
  without import issues
* ran the tests and no difference to the fixtures was detected

scripts/propka31.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+
+# This is the original propka script. However, this distribute-based
+# installation moved the main() function into propka.run.main and just
+# generates a script called propka31 from the setup.py installation
+# script. You should not need to use this script.
+#
+# (Also note that there can be import problems because the script name
+# is the same as the module name; that's why the new script is called
+# propka31.)
+
+import propka.lib, propka.molecular_container
+
+def main():
+    """
+    Reads in structure files, calculates pKa values, and prints pKa files
+    """
+    # loading options, flaggs and arguments
+    options, pdbfiles = propka.lib.loadOptions()
+
+    for pdbfile in pdbfiles:
+        my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+        my_molecule.calculate_pka()
+        my_molecule.write_pka()
+
+
+if __name__ == '__main__':
+    #import cProfile
+    #cProfile.run('main()',sort=1)
+    main()
+