Code linting and add test

peleffy/tests/test_main.py

@@ -171,6 +171,33 @@ def test_peleffy_argparse(self):
         assert parsed_args.with_solvent is False, \
             'Unexpected with_solvent settings were parsed'
 
+        # Test charges_from_file argument
+        parsed_args = parse_args(['BHP.pdb',
+                                  '--charges_from_file', 'BHP.mae'])
+
+        assert parsed_args.as_datalocal is False, \
+            'Unexpected as_datalocal settings were parsed'
+        assert parsed_args.charge_method == 'am1bcc', \
+            'Unexpected charge_method settings were parsed'
+        assert parsed_args.debug is False, \
+            'Unexpected debug settings were parsed'
+        assert parsed_args.forcefield == 'openff_unconstrained-1.3.0.offxml', \
+            'Unexpected forcefield settings were parsed'
+        assert parsed_args.include_terminal_rotamers is False, \
+            'Unexpected include_terminal_rotamers settings were parsed'
+        assert parsed_args.charges_from_file == 'BHP.mae', \
+            'Unexpected charges_from_file settings were parsed'
+        assert parsed_args.output is None, \
+            'Unexpected output settings were parsed'
+        assert parsed_args.pdb_file == 'BHP.pdb', \
+            'Unexpected pdb_file settings were parsed'
+        assert parsed_args.resolution == 30, \
+            'Unexpected resolution settings were parsed'
+        assert parsed_args.silent is False, \
+            'Unexpected silent settings were parsed'
+        assert parsed_args.with_solvent is False, \
+            'Unexpected with_solvent settings were parsed'
+
         # Test include_terminal_rotamers argument
         parsed_args = parse_args(['methane.pdb',
                                   '--include_terminal_rotamers'])

peleffy/utils/utils.py

@@ -224,6 +224,7 @@ def convert_all_quantities_to_string(data_structure):
 
     return obj_to_return
 
+
 def parse_charges_from_mae(path, parameters):
     """
     It reads an external file containing the partial charges to assign to the
@@ -245,8 +246,8 @@ def parse_charges_from_mae(path, parameters):
     import re
 
     # Read external file containing the partial charges information
-    params_info, params_list =([] for i in range(2))
-    copy =  False
+    params_info, params_list = ([] for i in range(2))
+    copy = False
     with open(path, 'r') as file:
         for line in file.readlines():
             if bool(re.match(r' m_atom\[(.*?)\] {', line)):
@@ -256,16 +257,16 @@ def parse_charges_from_mae(path, parameters):
                 type_data = 'params'
             if '}' in line:
                 copy = False
-            if copy == True and type_data == 'info':
+            if copy is True and type_data == 'info':
                 params_info.append(line)
-            if copy == True and type_data == 'params':
+            if copy is True and type_data == 'params':
                 params_list.append(line)
-        params_info = [ p.replace('\n', '').strip() for p in params_info[1:]]
+        params_info = [p.replace('\n', '').strip() for p in params_info[1:]]
         params_list = [l.replace('"', '').split() for l in params_list[1:-1]]
 
     # Get the index of the atom name and charge from the parameter's list
     idx_charges, idx_atom_name = (None for i in range(2))
-    for idx,line in enumerate(params_info):
+    for idx, line in enumerate(params_info):
         if 's_m_pdb_atom_name' in line:
             idx_atom_name = idx
         if 'r_m_charge1' in line:
@@ -285,15 +286,16 @@ def parse_charges_from_mae(path, parameters):
         atom_name = atom_name.replace('_', '')
         if atom_name in d:
             new_charges_parameters.append(unit.Quantity(
-                            value = float(d.get(atom_name)),
-                            unit = unit.elementary_charge))
+                value=float(d.get(atom_name)),
+                unit=unit.elementary_charge))
         else:
             raise ValueError(
                 "Molecule atom name {} does not match with ".format(atom_name)
                 + "any external file atom name's.")
     parameters['charges'] = new_charges_parameters
     return parameters
 
+
 class Logger(object):
     """
     It contains all the required methods to handle logging messages.