add modify_residue_number

analysis_pdb.py

@@ -145,6 +145,30 @@ class PDBAnalyzer:
 
         # Return a new instance of PDBAnalyzer pointing to the cleaned file
         return cls(out_file)
+    
+    def modify_residue_number(self, chain_id: str, original_res_num: int, new_res_num: int) -> PandasPdb:
+        """
+        Modify the residue number for a specific chain in a PDB file.
+        
+        Args:
+        chain_id (str): The chain identifier in the PDB file.
+        original_res_num (int): The original residue number to find.
+        new_res_num (int): The new residue number to replace with.
+        
+        Returns:
+        PandasPdb: The modified PDB structure as a PandasPdb object.
+        """
+        # Check if the residue number to be replaced exists
+        mask = (self.biodata.df['ATOM']['chain_id'] == chain_id) & \
+               (self.biodata.df['ATOM']['residue_number'] == original_res_num)
+        if not mask.any():
+            raise ValueError(f"Residue number {original_res_num} in chain {chain_id} does not exist in the PDB file.")
+        
+        # Update the residue number
+        self.biodata.df['ATOM'].loc[mask, 'residue_number'] = new_res_num
+
+        # Return the modified PandasPdb object
+        return self.biodata
 
     def extract_chains_to_new_pdb(self, chains: List[str]) -> PandasPdb:
         """