Merge pull request #74 from volkamerlab/fix-sitealign-bug

Fix SiteAlign definitions for THR (set charge 1 to 0)
volkamerlab · Jun 29, 2021 · 95f61ae · 95f61ae
2 parents 73ed8cf + 53b4a82
commit 95f61ae
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/kissim/definitions.py b/kissim/definitions.py
@@ -61,7 +61,7 @@
         "PHE": [3.0, 0.0, 0.0, 0.0, 1.0, 0.0],
         "PRO": [1.0, 0.0, 0.0, 0.0, 0.0, 1.0],
         "SER": [1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
-        "THR": [1.0, 1.0, 1.0, 1.0, 0.0, 1.0],
+        "THR": [1.0, 1.0, 1.0, 0.0, 0.0, 1.0],
         "TRP": [3.0, 1.0, 0.0, 0.0, 1.0, 0.0],
         "TYR": [3.0, 1.0, 1.0, 0.0, 1.0, 0.0],
         "VAL": [1.0, 0.0, 0.0, 0.0, 0.0, 1.0],

diff --git a/kissim/tests/encoding/test_fingerprint.py b/kissim/tests/encoding/test_fingerprint.py
@@ -102,7 +102,7 @@ def test_from_structure_klifs_id(self, structure_klifs_id, fingerprint):
 
     @pytest.mark.parametrize(
         "structure_klifs_id, values_array_mean",
-        [(109, 4.9905), (12347, 5.1622)],
+        [(109, 4.9885), (12347, 5.1590)],
     )
     def test_values_array(self, structure_klifs_id, values_array_mean):
         """
@@ -111,6 +111,8 @@ def test_values_array(self, structure_klifs_id, values_array_mean):
 
         fingerprint = Fingerprint.from_structure_klifs_id(structure_klifs_id, LOCAL)
         values_array_mean_calculated = np.nanmean(fingerprint.values_array(True, True, True))
+        print(fingerprint.values_array(True, True, True)[:8])
+        print(fingerprint.values_array(True, True, True)[17 * 8 : 18 * 8])
         assert pytest.approx(values_array_mean_calculated, abs=1e-4) == values_array_mean
 
         # Test the different lengths of the final fingerprint based on the selection of

diff --git a/kissim/tests/encoding/test_fingerprint_generator.py b/kissim/tests/encoding/test_fingerprint_generator.py
@@ -30,11 +30,11 @@ class TestFingerprintGenerator:
     @pytest.mark.parametrize(
         "structure_klifs_ids, klifs_session, n_cores, fingerprints_values_array_sum",
         [
-            ([110, 118], REMOTE, 1, 10152.4256),
-            ([110, 118], REMOTE, 2, 10152.4256),
-            ([110, 118], LOCAL, 1, 10152.4256),
-            ([110, 118], LOCAL, 2, 10152.4256),
-            ([110, 118], None, None, 10152.4256),
+            ([110, 118], REMOTE, 1, 10148.4256),
+            ([110, 118], REMOTE, 2, 10148.4256),
+            ([110, 118], LOCAL, 1, 10148.4256),
+            ([110, 118], LOCAL, 2, 10148.4256),
+            ([110, 118], None, None, 10148.4256),
         ],
     )
     def test_from_structure_klifs_id(
@@ -96,7 +96,7 @@ def test_from_structure_klifs_id(
 
     @pytest.mark.parametrize(
         "structure_klifs_ids, normalize, values_array_sum",
-        [([110, 118], False, 10152.4256), ([110, 118], True, 10152.4256)],
+        [([110, 118], False, 10148.4256), ([110, 118], True, 10148.4256)],
     )
     def test_to_from_json(self, structure_klifs_ids, normalize, values_array_sum):
         """