add argparse

modelbuilder.py

@@ -8,7 +8,7 @@
 @Email              :pylyzeng@gmail.com
 @version            :1.0
 '''
-
+import argparse  
 from dataclasses import dataclass, field
 from pathlib import Path
 import os
@@ -172,7 +172,27 @@ class LoopModelBuilder:
         self.pymol_instance.create(merged_object_name, ' or '.join(object_names))
         self.pymol_instance.save(output_file, merged_object_name)
 
+def main():
+    # 创建ArgumentParser对象
+    parser = argparse.ArgumentParser(description="Loop Model Builder for PDB files")
+    # 添加参数
+    parser.add_argument("pdb_file", type=str, help="Path to the PDB file")
+    parser.add_argument("--typestr", type=str, default="refine.very_fast", 
+                        help="Model refinement type (default: refine.very_fast)")
+    parser.add_argument("--output_dir", type=str, default=None, 
+                        help="Output directory (default: same as PDB file directory)")
+
+    # 解析参数
+    args = parser.parse_args()
+
+    # 调用LoopModelBuilder
+    pdb_path = Path(args.pdb_file).absolute()
+    output_dir = Path(args.output_dir).absolute() if args.output_dir else None
+
+    model_builder = LoopModelBuilder(pdb_file=pdb_path, output_dir=output_dir)
+    result_path = model_builder.run(typestr=args.typestr)
+
+    print(f"Modeling completed. Output file: {result_path}")
 
 if __name__ == "__main__":
-    l = LoopModelBuilder(Path('./2vlk.pdb'))
+    main()
-    l.run()