Merge 40402b0 into 4b7b904

oddt · Apr 10, 2020 · 5135da8 · 5135da8
2 parents 4b7b904 + 40402b0
commit 5135da8
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Showing 3 changed files with 19 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,5 @@
 ### Development version (Git)
+* Fix calculating similarity of SPLIF fingerprints
 
 ### Version 0.7 (2019-12-23)
 * Support recent RDKit and Openbabel

diff --git a/oddt/fingerprints.py b/oddt/fingerprints.py
@@ -693,12 +693,14 @@ def combinatorial_rmsd(reference, query):
         query_protein = query_pair['protein_coords']
         rmsd_ligand = combinatorial_rmsd(ref_ligand, query_ligand)
         rmsd_protein = combinatorial_rmsd(ref_protein, query_protein)
-        n_matching = ((rmsd_ligand < rmsd_cutoff) &
-                      (rmsd_protein < rmsd_cutoff)).sum()
-        numla += n_matching
-        numpa += n_matching
-        nula += (rmsd_ligand < rmsd_cutoff).sum()
-        nupa += (rmsd_protein < rmsd_cutoff).sum()
+        num_matching_ligand = (rmsd_ligand < rmsd_cutoff).any(axis=0).sum()
+        num_matching_protein = (rmsd_protein < rmsd_cutoff).any(axis=0).sum()
+        num_all_ligand = len(ref_ligand) + len(query_ligand) - num_matching_ligand
+        num_all_protein = len(ref_protein) + len(query_protein) - num_matching_protein
+        numla += num_matching_ligand
+        numpa += num_matching_protein
+        nula += num_all_ligand
+        nupa += num_all_protein
     if nula == 0 or nupa == 0:
         return 0.
     else:

diff --git a/tests/test_fingerprints.py b/tests/test_fingerprints.py
@@ -429,19 +429,19 @@ def test_splif_similarity():
         test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb')))
     receptor.protein = True
     receptor.addh(only_polar=True)
-    # print(outcome)
     ref = SPLIF(mols[0], receptor)
-    outcome = [similarity_SPLIF(ref, SPLIF(mol, receptor)) for mol in mols[1:]]
+    outcome = [similarity_SPLIF(ref, SPLIF(mol, receptor)) for mol in mols]
     if oddt.toolkit.backend == 'ob':
-        target_outcome = np.array([0.694,  0.639,  0.707,  0.657,  0.690,
-                                   0.450,  0.702,  0.477,  0.576,  0.669,
-                                   0.658,  0.714,  0.683,  0.585,  0.535,
-                                   0.611,  0.554,  0.665,  0.697])
+        target_outcome = np.array([1.000, 0.811, 0.690, 0.833, 0.654,
+                                   0.860, 0.373, 0.833, 0.389, 0.550,
+                                   0.790, 0.771, 0.915, 0.851, 0.525,
+                                   0.436, 0.701, 0.479, 0.743, 0.728])
     else:
-        target_outcome = np.array([0.694,  0.639,  0.707,  0.657,  0.690,
-                                   0.467,  0.702,  0.485,  0.599,  0.669,
-                                   0.658,  0.714,  0.683,  0.585,  0.535,
-                                   0.611,  0.554,  0.665,  0.697])
+        target_outcome = np.array([1.000, 0.811, 0.690, 0.833, 0.654,
+                                   0.860, 0.387, 0.833, 0.394, 0.572,
+                                   0.790, 0.771, 0.915, 0.851, 0.525,
+                                   0.436, 0.701, 0.479, 0.743, 0.728])
+
     assert_array_almost_equal(outcome, target_outcome, decimal=3)