Fix lint errors in orca, tobacco, and remove_solvent modules

Fix unused variable (F841) in orca.py and line-too-long (E501) in
create_linker_from_smiles.py and remove_solvent.py.

Author: tdpham2

src/matkit/orca/orca.py

@@ -7,4 +7,4 @@ def run_orca(
     run_type: str,
 ):
     profile = OrcaProfile(command=orca_command)
-    calc = ORCA(profile=profile)
+    _calc = ORCA(profile=profile)

src/matkit/tobacco/create_linker_from_smiles.py

@@ -150,7 +150,8 @@ def update_cif_with_connection_site(
 
     Args:
         input_cif: Path to input CIF file
-        connection_sites: List of atom labels to be converted to connection sites
+        connection_sites: List of atom labels to be
+            converted to connection sites
         output_cif: Path to output CIF file
     """
     # Read and clean input file
@@ -193,7 +194,8 @@ def update_cif_with_connection_site(
 
 
 def update_aromatic_bond(cif_in, cif_out):
-    """Update CIF file by converting single bonds in aromatic rings to aromatic bonds."""
+    """Update CIF: convert single bonds in aromatic rings
+    to aromatic bonds."""
     with open(cif_in, encoding="utf-8") as f:
         data = [line.strip() for line in f if line.strip()]
 
@@ -257,11 +259,20 @@ def smiles_to_cif(smiles, output_prefix="L1"):
     for i, atom in enumerate(struct):
         label = f"{atom.symbol}{i + 1}"
         x, y, z = np.round(scaled_pos[i], 5)
-        pos_block += f"{label:<10}{atom.symbol:<6}{x:<10}{y:<10}{z:<10}0.00000  Uiso   1.00      0.00000\n"
+        pos_block += (
+            f"{label:<10}{atom.symbol:<6}"
+            f"{x:<10}{y:<10}{z:<10}"
+            f"0.00000  Uiso   1.00      0.00000\n"
+        )
         indices, _ = nl.get_neighbors(i)
         for j in indices:
             d = struct.get_distance(i, j, mic=True)
-            bond_block += f"{label:<6}{struct[j].symbol}{j + 1:<6}{round(d, 4):<8}.     S\n"
+            jlabel = f"{struct[j].symbol}{j + 1}"
+            dist = round(d, 4)
+            bond_block += (
+                f"{label:<6}{jlabel:<6}"
+                f"{dist:<8}.     S\n"
+            )
 
     with open(final_cif, "w", encoding="utf-8") as f:
         f.write(

src/matkit/utils/remove_solvent.py

@@ -7,7 +7,8 @@
 
 
 def remove_solvent(path_to_cif, output_path, mass_ratio=0.8, skin=0.3):
-    """ Remove solvent, ions from a MOF using either chemical formula or ASE neighborlist
+    """Remove solvent, ions from a MOF using ASE
+    neighborlist
 
     Parameters:
         cif: str, absolute path to cif file
@@ -39,7 +40,8 @@ def remove_solvent(path_to_cif, output_path, mass_ratio=0.8, skin=0.3):
         g = list(g)
         fragment = atoms[g]
         fragment = sort(fragment)
-        massG.append(sum(atoms[g].get_masses())) # Mass of each disconnected subgraph
+        # Mass of each disconnected subgraph
+        massG.append(sum(atoms[g].get_masses()))
 
     max_index = np.argmax(massG)
     for index, mass in enumerate(massG):