Make PDB parser ignore self bodning

samirelanduk · Nov 2, 2017 · b9a439b · b9a439b
1 parent bbab26a
commit b9a439b
Show file tree

Hide file tree

Showing 2 changed files with 21 additions and 0 deletions.
diff --git a/atomium/files/pdbdict2pdb.py b/atomium/files/pdbdict2pdb.py
@@ -141,6 +141,9 @@ def make_connections_bonds(model, connections):
     :param list connections: The connections list from a data dictionary"""
 
     for connection in connections:
+        try:
+            connection["bond_to"].remove(connection["atom"])
+        except: pass
         atom = model.atom(atom_id=connection["atom"])
         if atom:
             for other in connection["bond_to"]:

diff --git a/tests/unit/files_tests/test_pdb_dict_to_pdb.py b/tests/unit/files_tests/test_pdb_dict_to_pdb.py
@@ -342,3 +342,21 @@ def test_can_bond_from_connections(self):
         atoms[2].bond.assert_called_with(atoms[1])
         atoms[3].bond.assert_called_with(atoms[1])
         self.assertFalse(atoms[0].called)
+
+
+    def test_can_ignore_self_bonding(self):
+        model = Mock()
+        atoms = [Mock(), Mock(), Mock(), Mock()]
+        model.atom.side_effect = [
+         atoms[0], atoms[1], atoms[2], atoms[3]
+        ]
+        for index, atom in enumerate(atoms):
+            atom.atom_id.return_value = index + 1
+            atom.bond = MagicMock()
+        connections = [{
+         "atom": 1, "bond_to": [1, 2, 3, 4]
+        }]
+        make_connections_bonds(model, connections)
+        atoms[0].bond.assert_any_call(atoms[1])
+        atoms[0].bond.assert_any_call(atoms[2])
+        atoms[0].bond.assert_called_with(atoms[3])