fixed Flake8 lint issues with whitespace

protein_design_tools/core/__init__.py

@@ -0,0 +1 @@
+# This file can be empty or contain initialization code for the package

protein_design_tools/core/protein_structure.py

@@ -150,7 +150,7 @@ def remove_residues_by_name(self, residue_name: str) -> None:
         ----------
         residue_name : str
             Residue name to be removed (e.g. 'HOH' for water).
-            
+
         """
         for chain in self.chains:
             # Keep only residues whose name != residue_name

protein_design_tools/io/__init__.py

@@ -0,0 +1 @@
+# This file can be empty or contain initialization code for the package

protein_design_tools/io/pdb.py

@@ -112,7 +112,7 @@ def _parse_pdb_content(
     -------
     ProteinStructure
         The populated ProteinStructure object.
-        
+
     """
     for line in content:
         if line.startswith("ATOM") or line.startswith("HETATM"):

protein_design_tools/utils/__init__.py

@@ -0,0 +1 @@
+# This file can be empty or contain initialization code for the package