residues in ss msg more accurate

ur-whitelab · Aug 6, 2024 · b1ed791 · b1ed791
1 parent 6cbf844
commit b1ed791
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Showing 2 changed files with 50 additions and 52 deletions.
diff --git a/mdagent/tools/base_tools/analysis_tools/secondary_structure.py b/mdagent/tools/base_tools/analysis_tools/secondary_structure.py
@@ -73,21 +73,21 @@ 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:

diff --git a/tests/test_analysis/test_secondary_structure.py b/tests/test_analysis/test_secondary_structure.py
@@ -17,13 +17,11 @@ 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
@@ -43,26 +41,26 @@ def test_dssp_codes(compute_dssp_simple, compute_dssp):
 
     nl_simple = compute_dssp_simple._dssp_natural_language()
     assert nl_simple == {
-        "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",
     }
 
     dssp_codes = compute_dssp._dssp_codes()
     assert dssp_codes == ["H", "B", "E", "G", "I", "T", "S", " ", "NA"]
 
     nl = compute_dssp._dssp_natural_language()
     assert nl == {
-        "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",
     }
 
 
@@ -71,49 +69,49 @@ def test_convert_dssp_counts(compute_dssp_simple, compute_dssp):
 
     descriptive_counts = compute_dssp_simple._convert_dssp_counts(dssp_counts)
     assert descriptive_counts == {
-        "helix": 0,
-        "strand": 5,
-        "coil": 5,
+        "residues in helix": 0,
+        "residues in strand": 5,
+        "residues in coil": 5,
     }
 
     dssp_counts = {"H": 0, "B": 0, "E": 5, "G": 0, "I": 0, "T": 0, "S": 0, " ": 5}
 
     descriptive_counts = compute_dssp._convert_dssp_counts(dssp_counts)
 
     assert descriptive_counts == {
-        "alpha helix": 0,
-        "beta bridge": 0,
-        "extended strand": 5,
-        "three helix": 0,
-        "five helix": 0,
-        "hydrogen bonded turn": 0,
-        "bend": 0,
-        "loop or irregular": 5,
+        "residues in alpha helix": 0,
+        "residues in beta bridge": 0,
+        "residues in extended strand": 5,
+        "residues in three helix": 0,
+        "residues in five helix": 0,
+        "residues in hydrogen bonded turn": 0,
+        "residues in bend": 0,
+        "residues in loop or irregular": 5,
     }
 
 
 def test_summarize_dssp(compute_dssp_simple, compute_dssp):
     dssp_array = np.array([["C", "C", "C", "E", "E", "E", "C", "C", "E", "E"]])
     summary = compute_dssp_simple._summarize_dssp(dssp_array)
     assert summary == {
-        "helix": 0,
-        "strand": 5,
-        "coil": 5,
-        "not assigned, not a protein residue": 0,
+        "residues in helix": 0,
+        "residues in strand": 5,
+        "residues in coil": 5,
+        "residues not assigned, not a protein residue": 0,
     }
 
     dssp_array = np.array([[" ", " ", " ", "E", "E", "E", "T", "T", "E", "E"]])
     summary = compute_dssp._summarize_dssp(dssp_array)
     assert summary == {
-        "alpha helix": 0,
-        "beta bridge": 0,
-        "extended strand": 5,
-        "three helix": 0,
-        "five helix": 0,
-        "hydrogen bonded turn": 2,
-        "bend": 0,
-        "loop or irregular": 3,
-        "not assigned, not a protein residue": 0,
+        "residues in alpha helix": 0,
+        "residues in beta bridge": 0,
+        "residues in extended strand": 5,
+        "residues in three helix": 0,
+        "residues in five helix": 0,
+        "residues in hydrogen bonded turn": 2,
+        "residues in bend": 0,
+        "residues in loop or irregular": 3,
+        "residues not assigned, not a protein residue": 0,
     }