change split chain path and modellerfix file path

modelbuilder.py

@@ -75,7 +75,7 @@ class LoopModelBuilder:
     def split_chains(self) -> dict:
         split_dict = {}
         for chain_id in self.analyzer_instance.chain_id_list:
-            chain_file = Path(f"{self.analyzer_instance.pid}_{chain_id}.pdb")
+            chain_file = self.output_dir.joinpath(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
@@ -160,7 +160,7 @@ class LoopModelBuilder:
         split_dict = self.split_all_chains()
         mc_dict = self.model_missing_loops(typestr=typestr)
         split_dict.update(mc_dict)  # 更新 split_dict
-        self.import_and_merge_pdb_strings(split_dict, "merged_object", f'{self.analyzer_instance.pid}.modellerfix.pdb')
+        self.import_and_merge_pdb_strings(split_dict, "merged_object", self.output_dir.joinpath(f'{self.analyzer_instance.pid}.modellerfix.pdb').as_posix())
 
     def import_and_merge_pdb_strings(self, pdb_strings, merged_object_name, output_file):
         # 使用 PyMOL 实例导入和合并 PDB