add logging

analysis_pdb.py

@@ -30,7 +30,8 @@ from copy import deepcopy
 from pymol import cmd
 from pymol import CmdException
 import pymol
-import os
+import logging
+from logging.handlers import RotatingFileHandler
 # 使用 BioPython 导入氨基酸缩写
 AMINO_ACIDS = set(IUPACData.protein_letters)
 
@@ -101,19 +102,32 @@ class PDBAnalyzer:
     biodf: PandasPdb = field(init=False)
     protein_state: str = field(init=False) # Apo or Holo
     chain_id_list: List[str] = field(init=False)
+    logger: logging.Logger = field(init=False)
 
     def __post_init__(self):
         """ 
         Initialize the PDB structure after the object is created.
         """
-        self.initialize_properties()
+        self._initialize_logging()
+        self._initialize_structure()
+        self._initialize_properties()
         
-    def initialize_properties(self):
+    def _initialize_logging(self):
+        self.logger = logging.getLogger(f"PDBAnalyzer_{self.pdb_file.stem}")
+        self.logger.setLevel(logging.DEBUG)
+        handler = RotatingFileHandler(f"{self.pdb_file.stem}.log", maxBytes=1048576, backupCount=5)
+        formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
+        handler.setFormatter(formatter)
+        self.logger.addHandler(handler)
+        
+    def _initialize_structure(self):
+        self.structure = PDBParser(QUIET=True).get_structure('PDB_structure', self.pdb_file.as_posix())
+        self.protein_structure = self.structure
+
+    def _initialize_properties(self):
         """Initialize properties based on the pdb_file."""
         self.pdb_file_stem = self.pdb_file.stem.split('.')[0]
         self.pid = self.pdb_file_stem.lower() if len(self.pdb_file_stem) == 4 else None
-        self.structure = PDBParser(QUIET=True).get_structure('PDB_structure', self.pdb_file.as_posix())
-        self.protein_structure = PDBParser(QUIET=True).get_structure('PDB_structure', self.pdb_file.as_posix())
         self.biodata = PandasPdb().read_pdb(self.pdb_file.as_posix())
         self.protein_state = 'Holo' if 'HETATM' in self.biodata.df.keys() else 'Apo'
         self.chain_id_list = self.biodata.df['ATOM']['chain_id'].drop_duplicates().to_list()