Change propka31 to propka32.

scripts/propka32.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+"""PROPKA script.
+
+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.)
+"""
+from propka.lib import loadOptions
+from propka.input import read_parameter_file, read_molecule_file
+from propka.parameters import Parameters
+from propka.molecular_container import MolecularContainer
+
+
+def main():
+    """Read in structure files, calculates pKa values, and prints pKa files."""
+    # loading options, flaggs and arguments
+    options = loadOptions([])
+    pdbfiles = options.filenames
+    parameters = read_parameter_file(options.parameters, Parameters())
+
+    for pdbfile in pdbfiles:
+        my_molecule = MolecularContainer(parameters, options)
+        my_molecule = read_molecule_file(pdbfile, my_molecule)
+        my_molecule.calculate_pka()
+        my_molecule.write_pka()
+        if options.generate_propka_input:
+            my_molecule.write_propka()
+
+
+if __name__ == '__main__':
+    main()