Replace optparse with argparse.

Optparse is deprecated.  Argparse will allow tighter integration with
PDB2PQR/APBS.

propka/run.py

@@ -1,13 +1,18 @@
 # entry point for propka script
-
+import logging
 import propka.lib, propka.molecular_container
 
+
+_LOGGER = logging.getLogger("PROPKA")
+
+
 def main():
     """
     Reads in structure files, calculates pKa values, and prints pKa files
     """
     # loading options, flaggs and arguments
-    options, pdbfiles = propka.lib.loadOptions()
+    options = propka.lib.loadOptions()
+    pdbfiles = options.filenames
 
     for pdbfile in pdbfiles:
         my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
@@ -25,7 +30,10 @@ def single(pdbfile, optargs=None):
        single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
     """
     optargs = optargs if optargs is not None else []
-    options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
+    options = propka.lib.loadOptions(*optargs)
+    pdbfile = options.filenames.pop(0)
+    if len(options.filenames) > 0:
+        _LOGGER.warning("Ignoring filenames: %s", options.filenames)
 
     my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
     my_molecule.calculate_pka()