update

Author: ajfriedman22

ensemble_md/replica_exchange_EE.py

@@ -164,6 +164,7 @@ def set_params(self, analysis):
             "resname_transform": None,
             "resname_list": None,
             "swap_rep_pattern": None,
+            "allow_virtual_V": True,
             "nst_sim": None,
             "proposal": 'exhaustive',
             "w_combine": False,
@@ -1720,7 +1721,7 @@ def process_top(self):
         function. Output as csv files to prevent needing to re-run this step.
         """
         if not os.path.exists('atom_name_mapping.csv') and self.resname_list is not None:
-            coordinate_swap.create_atom_map(self.gro, self.resname_list, self.swap_rep_pattern)
+            coordinate_swap.create_atom_map(self.gro, self.resname_list, self.swap_rep_pattern, self.allow_virtual_V)
             atom_name_mapping = pd.read_csv('atom_name_mapping.csv')
         elif self.resname_list is not None:
             atom_name_mapping = pd.read_csv('atom_name_mapping.csv')

ensemble_md/utils/coordinate_swap.py

@@ -1242,7 +1242,7 @@ def _read_gro(side, resname_list, gro_list):
     return name, num
 
 
-def create_atom_map(gro_list, resname_list, swap_patterns):
+def create_atom_map(gro_list, resname_list, swap_patterns, allow_virtual_V=True):
     """
     If you generate your hybrid topologies in a way that the
     same atom has the same name in each molecule then this
@@ -1287,6 +1287,7 @@ def create_atom_map(gro_list, resname_list, swap_patterns):
                 nb = nameB.index(f'D{element}{num}')
                 atomnameB.append(f'D{element}{num}')
                 atomidB.append(numB[nb])
+            
 
         df = pd.DataFrame({'resname A': resname_list[swap_pattern[0][0]], 'resname B': resname_list[swap_pattern[1][0]], 'atomid A': atomidA, 'atom name A': atomnameA, 'atomid B': atomidB, 'atom name B': atomnameB})  # noqa: E501
         output_df = pd.concat([output_df, df])