add pymol change_chain_identifier

analysis_pdb.py

@@ -25,11 +25,63 @@ from Bio.Align import PairwiseAligner
 import requests
 from copy import deepcopy
 from pymol import cmd
+from pymol import CmdException
 import pymol
 import os
 # 使用 BioPython 导入氨基酸缩写
 AMINO_ACIDS = set(IUPACData.protein_letters)
 
+class PyMOLInstance:
+    """
+    Class to handle a separate PyMOL instance.
+    """
+    def __init__(self):
+        self.cmd = pymol.cmd
+        self.cmd.reinitialize()
+
+    @classmethod
+    def change_chain_identifier(cls, pdb_file: Path, old_chain_id: str, new_chain_id: str, output_file: Path):
+        """
+        Change the identifier of a specific chain in a PDB file using PyMOL.
+
+        Args:
+        pdb_file (Path): Path of the PDB file.
+        old_chain_id (str): Original identifier of the chain.
+        new_chain_id (str): New identifier to be assigned to the chain.
+        output_file (Path): Path to save the modified PDB file.
+        """
+        cmd = pymol.cmd
+        cmd.reinitialize()
+        try:
+            cmd.load(pdb_file.as_posix(), "temp_structure")
+            cmd.alter(f'temp_structure and chain {old_chain_id}', f'chain="{new_chain_id}"')
+            cmd.save(output_file.as_posix(), "temp_structure")
+        except CmdException as e:
+            print(f"Error in PyMOL command: {e}")
+        finally:
+            cmd.delete("temp_structure")
+
+    def save(self, output_file: Path, format: str = 'pdb'):
+        """
+        Save the current state of the PyMOL instance to a file.
+
+        Args:
+        output_file (Path): Path to save the modified PDB file.
+        """
+        try:
+            self.cmd.save(filename=output_file.as_posix(), selection="temp_structure", format=format)
+        finally:
+            self.cmd.delete("temp_structure")
+
+# 使用示例
+def PyMOLInstance_change_chain_identifier(pdb_file_path: Path, old_chain_id: str, new_chain_id: str, output_file_path: Path):
+    # pdb_file_path = Path("path/to/your/pdb_file.pdb") # 更改为实际的文件路径
+    # old_chain_id = "A"
+    # new_chain_id = "D"
+    # output_file_path = Path("path/to/your/output_file.pdb")  # 更改为希望保存的输出路径
+    a = PyMOLInstance.change_chain_identifier(pdb_file_path, old_chain_id, new_chain_id, output_file_path)
+    a.save(output_file_path)
+
 @dataclass
 class PDBAnalyzer:
     """