update utils

Author: ajfriedman22

ensemble_md/utils/coordinate_swap.py

@@ -442,7 +442,7 @@ def get_miss_coord(mol_align, mol_ref, name_align, name_ref, df_atom_swap, dir,
         for a in range(mol_align_select.n_atoms):
             if a != conn0_align:
                 mol_align_select.xyz[0, a, :] = _rotate_point_around_axis(mol_align_select.xyz[0, a, :], mol_ref_select.xyz[0, conn0_ref, :], axis_rot, theta_min)  # noqa: E501
-
+        
         # Add coordinates to df
         for r in range(len(df_atom_swap.index)):
             if df_atom_swap.iloc[r]['Direction'] == 'miss' and df_atom_swap.iloc[r]['Swap'] == dir:
@@ -1184,7 +1184,7 @@ def get_names(input, resname):
                 continue
             while '' in line_sep:
                 line_sep.remove('')
-            if line_sep[0] == '\n':
+            if line_sep[0] == '\n' or line == '[ bonds ]\n':
                 start_line = l+2
                 break
             if line_sep[3] == resname:

ensemble_md/utils/gmx_parser.py

@@ -438,7 +438,7 @@ def deter_atom_order(mol_file, resname):
             split_line.remove('')
         if resname in split_line[0]:
             if len(split_line[1]) > 5:
-                split_line = coordinate_swap.sep_merge(split_line)
+                split_line = coordinate_swap._sep_merge(split_line)
             atom_order.append(split_line[1])
         elif len(atom_order) != 0:
             break