formatting

mdagent/tools/base_tools/analysis_tools/secondary_structure.py

@@ -51,11 +51,13 @@ class ComputeDSSP(BaseTool):
     simplified: bool = True
     last_only: bool = True
 
-    def __init__(self, path_registry: PathRegistry, simplified: bool = True, last_only=True):
+    def __init__(
+        self, path_registry: PathRegistry, simplified: bool = True, last_only=True
+    ):
         super().__init__()
         self.path_registry = path_registry
         self.simplified = simplified
-        self.last_only=last_only
+        self.last_only = last_only
 
     def _dssp_codes(self) -> list[str]:
         """
@@ -162,7 +164,7 @@ def _run(self, traj_file: str, top_file: Optional[str] = None) -> str:
             )
             if not traj:
                 raise Exception("Trajectory could not be loaded.")
-            if self.last_only and len(traj)>1:
+            if self.last_only and len(traj) > 1:
                 traj = traj[-1]
         except Exception as e:
             print("Error loading trajectory: ", e)

tests/test_analysis/test_secondary_structure.py

@@ -17,11 +17,13 @@ def compute_dssp_simple(get_registry):
     registry = get_registry("raw", True)
     return ComputeDSSP(path_registry=registry, simplified=True)
 
+
 @pytest.fixture
 def compute_dssp(get_registry):
     registry = get_registry("raw", True)
     return ComputeDSSP(path_registry=registry, simplified=False)
 
+
 def test_compute_dssp(loaded_cif_traj, compute_dssp_simple, compute_dssp):
     dssp_simple = compute_dssp_simple._compute_dssp(loaded_cif_traj)
     assert dssp_simple.shape[1] == 374