De-lint run.py.

propka/run.py

@@ -1,24 +1,24 @@
-# entry point for propka script
+"""Entry point for PROPKA script."""
 import logging
-import propka.lib, propka.molecular_container
+from propka.lib import loadOptions
+from propka.molecular_container import 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 = propka.lib.loadOptions()
+def main(optargs=None):
+    """Read in structure files, calculate pKa values, and print pKa files."""
+    # loading options, flags and arguments
+    optargs = optargs if optargs is not None else []
+    options = loadOptions(*optargs)
     pdbfiles = options.filenames
-
     for pdbfile in pdbfiles:
-        my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
+        my_molecule = Molecular_container(pdbfile, options)
         my_molecule.calculate_pka()
         my_molecule.write_pka()
 
+
 def single(pdbfile, optargs=None):
     """Run a single PROPKA calculation using *pdbfile* as input.
 
@@ -30,12 +30,11 @@ 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 = propka.lib.loadOptions(*optargs)
+    options = 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 = Molecular_container(pdbfile, options)
     my_molecule.calculate_pka()
     my_molecule.write_pka()
     return my_molecule