fixed bugs in unittests for multi-chain permutation. now working on extra subtests

tests/test_permutation.py

@@ -55,7 +55,8 @@ class TestPermutation(unittest.TestCase):
         self.sym_id = self.asym_id
         self.entity_id = torch.tensor([[1] * (self.chain_a_num_res * 2) + [2] * (self.chain_b_num_res * 3)],
                                       device=device)
-
+    
+    # @unittest.skip("skip for now")
     def test_1_selecting_anchors(self):
         batch = {
             'asym_id': self.asym_id,
@@ -75,6 +76,7 @@ class TestPermutation(unittest.TestCase):
         self.assertEqual(anchor_pred_asym, expected_anchors & anchor_pred_asym)
         self.assertEqual(set(), anchor_pred_asym & expected_non_anchors) 
 
+    # @unittest.skip("skip for now")
     def test_2_permutation_pentamer(self):
         batch = {
             'asym_id': self.asym_id,
@@ -111,26 +113,25 @@ class TestPermutation(unittest.TestCase):
         batch['all_atom_positions'] = true_atom_position
         batch['all_atom_mask'] = true_atom_mask
 
-        aligns, _ = compute_permutation_alignment(out, batch,
+        aligns, per_asym_residue_index = compute_permutation_alignment(out, batch,
                                                   batch)
-        print(f"##### aligns is {aligns}")
         possible_outcome = [[(0, 1), (1, 0), (2, 3), (3, 4), (4, 2)], [(0, 0), (1, 1), (2, 3), (3, 4), (4, 2)]]
         wrong_outcome = [[(0, 1), (1, 0), (2, 4), (3, 2), (4, 3)], [(0, 0), (1, 1), (2, 2), (3, 3), (4, 4)]]
         self.assertIn(aligns, possible_outcome)
         self.assertNotIn(aligns, wrong_outcome)
 
-    @unittest.skip("Test needs to be fixed post-refactor")
+    # @unittest.skip("Test needs to be fixed post-refactor")
     def test_3_merge_labels(self):
         nres_pad = 325 - 57  # suppose the cropping size is 325
         batch = {
-            'asym_id': pad_features(self.asym_id, nres_pad, pad_dim=1),
-            'sym_id': pad_features(self.sym_id, nres_pad, pad_dim=1),
-            'entity_id': pad_features(self.entity_id, nres_pad, pad_dim=1),
-            'aatype': torch.randint(21, size=(1, 325)),
+            'asym_id': self.asym_id,
+            'sym_id': self.sym_id,
+            'entity_id': self.entity_id,
+            'aatype': torch.randint(21, size=(1, 57)),
             'seq_length': torch.tensor([57])
         }
-        batch['asym_id'] = batch['asym_id'].reshape(1, 325)
-        batch["residue_index"] = pad_features(torch.tensor(self.residue_index).reshape(1, 57), nres_pad, pad_dim=1)
+        batch['asym_id'] = batch['asym_id'].reshape(1, 57)
+        batch["residue_index"] = torch.tensor([self.residue_index])
         # create fake ground truth atom positions        
         chain_a1_pos = torch.randint(15, (self.chain_a_num_res, 3 * 37),
                                      dtype=torch.float).reshape(1, self.chain_a_num_res, 37, 3)
@@ -155,15 +156,30 @@ class TestPermutation(unittest.TestCase):
                                     torch.ones((1, self.chain_b_num_res, 37)),
                                     torch.ones((1, self.chain_b_num_res, 37)),
                                     torch.ones((1, self.chain_b_num_res, 37))), dim=1)
-        batch['all_atom_positions'] = pad_features(true_atom_position, nres_pad, pad_dim=1)
-        batch['all_atom_mask'] = pad_features(true_atom_mask, nres_pad=nres_pad, pad_dim=1)
 
-        # tensor_to_cuda = lambda t: t.to('cuda')
-        # ground_truth = tensor_tree_map(tensor_to_cuda,ground_truth)
+        batch['all_atom_positions'] = true_atom_position 
+        batch['all_atom_mask'] = true_atom_mask 
+
+        # Below create a fake_input_features 
+        fake_input_features  = {
+            'asym_id': pad_features(self.asym_id, nres_pad, pad_dim=1),
+            'sym_id': pad_features(self.sym_id, nres_pad, pad_dim=1),
+            'entity_id': pad_features(self.entity_id, nres_pad, pad_dim=1),
+            'aatype': torch.randint(21, size=(1, 325)),
+            'seq_length': torch.tensor([57])
+        }
+        fake_input_features['asym_id'] = fake_input_features['asym_id'].reshape(1, 325)
+        fake_input_features["residue_index"] = pad_features(torch.tensor(self.residue_index).reshape(1, 57), nres_pad, pad_dim=1)
+        fake_input_features['all_atom_positions'] = pad_features(true_atom_position, nres_pad, pad_dim=1)
+        fake_input_features['all_atom_mask'] = pad_features(true_atom_mask, nres_pad=nres_pad, pad_dim=1)
+        
+        # NOTE
+        # batch: simulates ground_truth features 
+        # fake_input_features: simulates the data that gonna be used as input for model.forward(fake_input_features)
+        # out: simulates the output of model.forward(fake_input_features)
         aligns, per_asym_residue_index = compute_permutation_alignment(out,
-                                                                       batch,
+                                                                       fake_input_features,
                                                                        batch)
-        print(f"##### aligns is {aligns}")
         labels = split_ground_truth_labels(batch)
 
         labels = merge_labels(per_asym_residue_index, labels, aligns,
@@ -173,5 +189,5 @@ class TestPermutation(unittest.TestCase):
 
         expected_permutated_gt_pos = torch.cat((chain_a2_pos, chain_a1_pos, chain_b2_pos, chain_b3_pos, chain_b1_pos),
                                                dim=1)
-        expected_permutated_gt_pos = pad_features(expected_permutated_gt_pos, nres_pad, pad_dim=1)
+        # expected_permutated_gt_pos = pad_features(expected_permutated_gt_pos, nres_pad, pad_dim=1)
         self.assertTrue(torch.equal(labels['all_atom_positions'], expected_permutated_gt_pos))