secondary structure analysis fix

mdagent/tools/base_tools/analysis_tools/rgy.py

@@ -1,3 +1,4 @@
+import os
 from typing import Optional
 
 import matplotlib.pyplot as plt
@@ -80,16 +81,25 @@ def plot_rad_gyration(self, pdb_id: str) -> str:
         plot_id = self.path_registry.get_fileid(
             file_name=plot_name, type=FileType.FIGURE
         )
+        if plot_name.ends_with(".png"):
+            plot_name = plot_name.split(".png"[0])
+        plot_path = next(
+            f"{self.path_registry.ckpt_figures}/{plot_name}_{i}.png"
+            for i in range(1000)
+            if not os.path.exists(
+                f"{self.path_registry.ckpt_figures}/{plot_name}_{i}.png"
+            )
+        )
 
         plt.plot(rg_per_frame)
         plt.xlabel("Frame")
         plt.ylabel("Radius of Gyration (nm)")
         plt.title(f"{pdb_id} - Radius of Gyration Over Time")
 
-        plt.savefig(f"{self.path_registry.ckpt_figures}/{plot_name}")
+        plt.savefig(f"{plot_path}")
         self.path_registry.map_path(
             plot_id,
-            f"{self.path_registry.ckpt_figures}/{plot_name}",
+            plot_path,
             description=f"Plot of radii of gyration over time for {self.pdb_id}",
         )
         plt.close()

mdagent/tools/base_tools/analysis_tools/secondary_structure.py

@@ -49,11 +49,15 @@ class ComputeDSSP(BaseTool):
     residue at each time point."""
     path_registry: PathRegistry = PathRegistry.get_instance()
     simplified: bool = True
+    last_only: bool = True
 
-    def __init__(self, path_registry: PathRegistry, simplified: bool = 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
 
     def _dssp_codes(self) -> list[str]:
         """
@@ -71,21 +75,21 @@ def _dssp_natural_language(self) -> dict[str, str]:
         used. Otherwise, the full set of codes is used."""
         if self.simplified:
             return {
-                "H": "helix",
-                "E": "strand",
-                "C": "coil",
-                "NA": "not assigned, not a protein residue",
+                "H": "residues in helix",
+                "E": "residues in strand",
+                "C": "residues in coil",
+                "NA": "residues not assigned, not a protein residue",
             }
         return {
-            "H": "alpha helix",
-            "B": "beta bridge",
-            "E": "extended strand",
-            "G": "three helix",
-            "I": "five helix",
-            "T": "hydrogen bonded turn",
-            "S": "bend",
-            " ": "loop or irregular",
-            "NA": "not assigned, not a protein residue",
+            "H": "residues in alpha helix",
+            "B": "residues in beta bridge",
+            "E": "residues in extended strand",
+            "G": "residues in three helix",
+            "I": "residues in five helix",
+            "T": "residues in hydrogen bonded turn",
+            "S": "residues in bend",
+            " ": "residues in loop or irregular",
+            "NA": "residues not assigned, not a protein residue",
         }
 
     def _convert_dssp_counts(self, dssp_counts: dict) -> dict:
@@ -160,6 +164,8 @@ 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:
+                traj = traj[-1]
         except Exception as e:
             print("Error loading trajectory: ", e)
             return str(e)