From 296c1815929592d3bd9da851608da5e98b5dc990 Mon Sep 17 00:00:00 2001
From: Anika <anika.friedman@gmail.com>
Date: Thu, 10 Oct 2024 12:47:10 -0600
Subject: [PATCH] Fix linting error

---
 ensemble_md/utils/coordinate_swap.py | 5 +----
 ensemble_md/utils/gmx_parser.py      | 6 +++---
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/ensemble_md/utils/coordinate_swap.py b/ensemble_md/utils/coordinate_swap.py
index 18c10a5..f96e505 100644
--- a/ensemble_md/utils/coordinate_swap.py
+++ b/ensemble_md/utils/coordinate_swap.py
@@ -708,9 +708,6 @@ def dummy_real_swap(mol_new, resnum, resname, df, vel, atom_num, orig_coords, na
         Since the atom may be added in a different order than it was in the previous file save the line
         number so that we skip it when we come to it.
     """
-    # Get the name for the atom we are writting
-    name_orig = df['Name'].to_list()[0]
-
     # These may be added out of order so lets make sure we have the right coordinates
     line_num = df['File line'].to_list()[0]
     c = line_num - 2
@@ -991,7 +988,7 @@ def write_new_file(df_atom_swap, swap, r_swap, line_start, orig_file, new_file,
                 atom_num_B -= 1
                 atom_num_A += 1
                 continue
-            elif line[1] == atom_order[res_interest_atom]:  # Just change atom or residue number as needed since atom is in the right order
+            elif line[1] == atom_order[res_interest_atom]:  # Just change atom or residue number as needed since atom is in the right order  # noqa: E501
                 write_line(new_file, orig_file[i], line, atom_num_B, vel, orig_coords[atom_num_A], resnum, new_res_name)  # noqa: E501
                 res_interest_atom += 1
             elif (f'{current_element}{current_num}' == atom_order[res_interest_atom]) or (f'{current_element}V{current_num}' == atom_order[res_interest_atom]) or (f'D{current_element}{current_num}' == atom_order[res_interest_atom]):  # Since atom is not in missing it must be a D2R flip  # noqa: E501
diff --git a/ensemble_md/utils/gmx_parser.py b/ensemble_md/utils/gmx_parser.py
index 3b11bd4..4ee8eb3 100644
--- a/ensemble_md/utils/gmx_parser.py
+++ b/ensemble_md/utils/gmx_parser.py
@@ -415,7 +415,7 @@ def read_top(file_name, resname):
 def deter_atom_order(mol_file, resname):
     """
     Determine the order of atoms in the residue we will modify to ensure the output GRO is formatted properly
-    
+
     Parameters
     ----------
     file_name : list of str
@@ -427,7 +427,7 @@ def deter_atom_order(mol_file, resname):
     -------
     atom_order : list of str
         List of the atom names in the order they appear in the GRO file
-    
+
     """
     from ensemble_md.utils import coordinate_swap
 
@@ -442,5 +442,5 @@ def deter_atom_order(mol_file, resname):
             atom_order.append(split_line[1])
         elif len(atom_order) != 0:
             break
-            
+
     return atom_order