dssp incompleate residues fix

pegerto · Oct 9, 2024 · 073a938 · 073a938
1 parent 71b41e4
commit 073a938
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Showing 3 changed files with 12,746 additions and 3 deletions.
diff --git a/src/graphpro/util/dssp.py b/src/graphpro/util/dssp.py
@@ -31,7 +31,7 @@ def compute_dssp(atom_group: AtomGroup):
             if iatom not in visited:
                 visited.append(iatom)
                 atoms.append(atom.position)
-    if atoms:
+    if atoms and len(atoms) >= 4: # not adding partial residue atoms
         coords.append(np.array(atoms))
 
     npcoords = np.array(coords)

diff --git a/test/graphpro/annnotations/dssp_test.py b/test/graphpro/annnotations/dssp_test.py
@@ -13,6 +13,10 @@
         os.path.realpath(__file__)) +
     '/../../testdata/4aw0.pdb')
 
+u3 = mda.Universe(
+    os.path.dirname(
+        os.path.realpath(__file__)) +
+    '/../../testdata/1w96.pdb')
 
 def test_dssp():
     G = md_analisys(u1).generate(ContactMap(cutoff=6), [DSSP()])
@@ -24,7 +28,16 @@ def test_dssp_multiple_occupancies():
     G = md_analisys(u2).generate(ContactMap(cutoff=6), [DSSP()])
     assert len(G.nodes()) == 283
 
-def test_encode_enconde():
+def test_dssp_incompleted_resiude():
+    G = md_analisys(u3).generate(ContactMap(cutoff=6), [DSSP()])
+    assert len(G.nodes()) == 554
+
+def test_dssp_enconde():
     G = md_analisys(u1).generate(ContactMap(cutoff=6), [DSSP()])
     data = G.to_data(node_encoders=[DSSP()])
-    assert data.x.size() == (13,3)
+    assert data.x.size() == (13,3)
+
+def test_dssp_encode_incompleted():
+    G = md_analisys(u3).generate(ContactMap(cutoff=6), [DSSP()])
+    data = G.to_data(node_encoders=[DSSP()])
+    assert data.x.size() == (554,3)