add no fix situation

modelbuilder.py

@@ -51,15 +51,12 @@ class LoopModelBuilder:
     logger: logging.Logger = field(init=False)
     pymol_instance: object = field(init=False)
     analyzer_instance: PDBAnalyzer = field(init=False)
-    runner_dir: Path = field(init=False)
     pdb_id: str = field(init=False)
 
     def __post_init__(self):
         self.pdb_id = self.pdb_file.stem
         self.output_dir = self.pdb_file.parent if self.output_dir is None else self.output_dir
-        self.runner_dir = self.output_dir / f"runner_{self.pdb_id}"
         self.analyzer_instance = PDBAnalyzer(self.pdb_file)
-        self.initialize_workdir()
         self.setup_logging()
         self.initialize_pymol()
 
@@ -75,15 +72,10 @@ class LoopModelBuilder:
         self.pymol_instance = pymol.cmd
         self.pymol_instance.reinitialize()
 
-    def initialize_workdir(self):
-        runner_dir = self.output_dir / f"runner_{self.pdb_file.stem}"
-        runner_dir.mkdir(exist_ok=True, parents=True)
-        self.runner_dir = runner_dir
-
     def split_chains(self) -> dict:
         split_dict = {}
         for chain_id in self.analyzer_instance.chain_id_list:
-            chain_file = self.runner_dir / f"{self.analyzer_instance.pid}_{chain_id}.pdb"
+            chain_file = Path(f"{self.analyzer_instance.pid}_{chain_id}.pdb")
             self.analyzer_instance.split_chain(chain_id).to_pdb(chain_file.as_posix())
             split_dict[chain_id] = chain_file.read_text()
         return split_dict
@@ -98,7 +90,7 @@ class LoopModelBuilder:
         self.merge_and_save_pdb(split_dict, pdb_id)
 
     def merge_and_save_pdb(self, pdb_strings: dict, pdb_id: str):
-        merged_file = self.runner_dir / f"{pdb_id}_merged.pdb"
+        merged_file = Path(f"{pdb_id}_merged.pdb")
         self.import_and_merge_pdb_strings(pdb_strings, "merged_object", merged_file)
 
     @property
@@ -110,10 +102,8 @@ class LoopModelBuilder:
         return self.analyzer_instance.extract_sequences_info()
 
     def split_all_chains(self):
-        sequences = self.analyzer_instance.extract_sequences(missing_char='-')  # 或者 'X', 或者 ''
+        self.logger.info(f'Residues info for {self.pdb_file}: \n',self.sequences)
-        self.logger.info(f'Residues info for {self.pdb_file}: \n',sequences)
+        self.logger.info(f'Missing residues info for {self.pdb_file}:\n {self.missing_info}')
-        missing_info = self.analyzer_instance.extract_sequences_info()
-        self.logger.info(f'Missing residues info for {self.pdb_file}:\n {missing_info}')
         split_dict = {} # split all chains
         for j in self.analyzer_instance.chain_id_list:
             fn = Path(f'{self.pdb_file.stem}_{j}.pdb')
@@ -123,6 +113,9 @@ class LoopModelBuilder:
 
     def model_missing_loops(self, typestr:str = 'refine.very_fast') -> dict:
         mc_dict = {}
+        if not self.missing_info:
+            self.logger.info(f'No missing residues found in {self.pdb_file}. Skipping model_missing_loops.')
+            return mc_dict
         for mc in self.missing_info:
             out_file = f'5sws_{mc}.pdb'
             self.analyzer_instance.split_chain(mc).to_pdb(out_file) # get misschain pdb file
@@ -156,7 +149,7 @@ class LoopModelBuilder:
                     mc_dict[mc] = pdbstr
                     return mc_dict
                 else:
-                    print('more than one model file, please set num_loop to 1')
+                    self.logger.warning('more than one model file, please set num_loop to 1')
             elif len(mc_fasta) == 0:
                 self.logger.warning(f'No chain {mc} found in PDB fasta file. Skipping chain {mc}.')
                 continue
@@ -181,5 +174,5 @@ class LoopModelBuilder:
 
 
 if __name__ == "__main__":
-    l = LoopModelBuilder(Path('./pdb_test1/1ao7.pdb'))
+    l = LoopModelBuilder(Path('./2vlk.pdb'))
     l.run()