Merge remote-tracking branch 'upstream/master' into nathan/strings

README.md

@@ -9,9 +9,9 @@ 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.
+* 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. doi:[10.1021/ct200133y](https://doi.org/10.1021/ct200133y)
 
-* 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.
+* 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. doi:[10.1021/ct100578z](https://doi.org/10.1021/ct100578z)
 
 See [propka.ki.ku.dk](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).

propka/__main__.py

@@ -0,0 +1,8 @@
+"""Allow the PROPKA package to be run as a program.
+
+For example, `python -m propka`
+"""
+from .run import main
+
+if __name__ == "__main__":
+    main()

propka/lib.py

@@ -279,10 +279,10 @@ def build_parser(parser=None):
     return parser
 
 
-def loadOptions(args):
-    """Load the arguments parser with options.
-
-    NOTE - verbosity is set as soon as this function is invoked.
+def loadOptions(args=None):
+    """
+    Load the arguments parser with options. Note that verbosity is set as soon
+    as this function is invoked.
 
     Arguments:
         args:  list of arguments
@@ -292,11 +292,8 @@ def loadOptions(args):
     # loading the parser
     parser = build_parser()
     # parsing and returning options and arguments
-    if len(args) == 0:
-        # command line
-        options = parser.parse_args()
-    else:
-        options = parser.parse_args(args)
+    options = parser.parse_args(args)
+
     # adding specified filenames to arguments
     options.filenames.append(options.input_pdb)
     # Convert titrate_only string to a list of (chain, resnum) items: