update PDBAlign

analysis_pdb.py

@@ -23,6 +23,7 @@ from Bio import SeqIO
 import requests
 from copy import deepcopy
 from pymol import cmd
+import pymol
 import os
 
 @dataclass
@@ -296,18 +297,26 @@ class PDBAnalyzer:
 class PDBAlign:
     template_file: Path
     target_file: Path  
+    pymol_instance: object = field(init=False)
     out_file: Path = field(default=None)  # 输出文件路径
 
+    def __post_init__(self):
+        self.initialize_pymol()
+
+    def initialize_pymol(self):
+        self.pymol_instance = pymol.cmd
+        self.pymol_instance.reinitialize()
+
     def align(self):
-        cmd.reinitialize()
+        self.pymol_instance.reinitialize()
         # 首先，加载模板结构
-        cmd.load(self.template_file.as_posix(), "template")
+        self.pymol_instance.load(self.template_file.as_posix(), "template")
 
         # 加载并对齐所有目标结构
-        cmd.load(self.target_file.as_posix(), "target")
+        self.pymol_instance.load(self.target_file.as_posix(), "target")
-        cmd.align("target", "template")
+        self.pymol_instance.align("target", "template")
 
-        return cmd.get_pdbstr('target')
+        return self.pymol_instance.get_pdbstr('target')
 
 def main(PDB_ID, PDB_file_path):
     # 示例
@@ -498,3 +507,4 @@ if __name__ == "__main__":
     pass
 
 
+