test cases updated in response to @biochunan's code adjustments

rigdenlab · Jul 25, 2017 · 32e8afc · 32e8afc
1 parent 3f5a805
commit 32e8afc
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Showing 2 changed files with 14 additions and 5 deletions.
diff --git a/conkit/core/contactmap.py b/conkit/core/contactmap.py
@@ -467,9 +467,11 @@ def calculate_kernel_density(self, bw_method="amise"):
             print("The ContactMap is empty!")
             return []
 
-        # Compute the ranges between each contact pair and store it
-	# REM: Bug in Sadowski's algorithm, fix in commented line below but untested/not optimized
+	# REM: Bug in Sadowski's algorithm, res2 is excluded from list to train KDE
+        # REM: Remember to change test cases when corrected implementation benchmarked
         #x = np.asarray([i for c in self for i in np.arange(c.res1_seq, c.res2_seq + 1)])[:, np.newaxis]
+
+        # Compute the ranges between each contact pair and store it
         x = np.asarray([i for c in self for i in np.arange(c.res1_seq, c.res2_seq)])[:, np.newaxis]
         # Compute per-residue points for density extraction
         x_fit = np.arange(x.min(), x.max() + 1)[:, np.newaxis]

diff --git a/conkit/core/tests/test_contactmap.py b/conkit/core/tests/test_contactmap.py
@@ -228,14 +228,21 @@ def test_calculate_jaccard_score_4(self):
         jindex = contact_map1.calculate_jaccard_index(contact_map2)
         self.assertEqual(1.0, jindex)
 
+    # REM: Bug in Sadowski res2(+1) error results in tests to fail. 
+    # REM: For now, code reverted by @biochunan to match Sadowski's implementation
+    # REM: Corresponding results for tests 1-3 are below when code is reverted to correct implementation
+    # REM: [0.11944664492151888, 0.20124328187327287, 0.23868489948868032, 0.20124328187327284, 0.11944664492151894]
+    # REM: [0.10012592274179978, 0.19837169506444377, 0.26841488628499205, 0.23132109484153407, 0.1217899243718511]
+    # REM: [0.14422964774244934, 0.4134215939843202, 0.41342159398432, 0.14422964774244929]
+
     @skipUnless(SKLEARN)
     def test_calculate_kernel_density_1(self):
         contact_map1 = ContactMap('foo')
         for c in [Contact(1, 5, 1.0), Contact(3, 3, 0.4), Contact(2, 4, 0.1)]:
             contact_map1.add(c)
         density = contact_map1.calculate_kernel_density()
         self.assertEqual(
-            [0.11944664492151888, 0.20124328187327287, 0.23868489948868032, 0.20124328187327284, 0.11944664492151894],
+            [0.16474084813765252, 0.24964700349773153, 0.24964700349773153, 0.16474084813765252],
             density)
 
     @skipUnless(SKLEARN)
@@ -245,7 +252,7 @@ def test_calculate_kernel_density_2(self):
             contact_map1.add(c)
         density = contact_map1.calculate_kernel_density()
         self.assertEqual(
-            [0.10012592274179978, 0.19837169506444377, 0.26841488628499205, 0.23132109484153407, 0.1217899243718511],
+            [0.14936186609839505, 0.26262219502283973, 0.2868154978059642, 0.1768745614827941],
             density)
 
     @skipUnless(SKLEARN)
@@ -254,7 +261,7 @@ def test_calculate_kernel_density_3(self):
         for c in [Contact(3, 5, 0.4), Contact(2, 4, 0.1), Contact(3, 4, 0.4)]:
             contact_map1.add(c)
         density = contact_map1.calculate_kernel_density()
-        self.assertEqual([0.14422964774244934, 0.4134215939843202, 0.41342159398432, 0.14422964774244929], density)
+        self.assertEqual([0.2282135747320191, 0.6337372073257503, 0.2282135747320191], density)
 
     def test_find_1(self):
         contact_map1 = ContactMap('1')