Merge pull request #556 from csbrasnett/mutate-fix

add warning when mod not found
marrink-lab · Oct 23, 2023 · 1593bf1 · 1593bf1
2 parents 0459973 + 9656689
commit 1593bf1
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Showing 2 changed files with 48 additions and 6 deletions.
diff --git a/vermouth/processors/annotate_mut_mod.py b/vermouth/processors/annotate_mut_mod.py
@@ -210,10 +210,12 @@ def annotate_modifications(molecule, modifications, mutations):
                     (mutations, 'mutation', molecule.force_field.blocks)]
 
     residue_graph = make_residue_graph(molecule)
-    for res_idx in residue_graph:
-        for mutmod, key, library in associations:
-            for resspec, mod in mutmod:
+    for mutmod, key, library in associations:
+        for resspec, mod in mutmod:
+            mod_found = False
+            for res_idx in residue_graph:
                 if residue_matches(resspec, residue_graph, res_idx):
+                    mod_found = True
                     if mod != 'none' and mod not in library:
                         raise NameError('{} is not known as a {} for '
                                         'force field {}'
@@ -223,7 +225,10 @@ def annotate_modifications(molecule, modifications, mutations):
                                  _format_resname(res), key, mod)
                     for node_idx in res['graph']:
                         molecule.nodes[node_idx][key] = molecule.nodes[node_idx].get(key, []) + [mod]
-
+            if mod_found == False:
+                LOGGER.warning('Mutation "{}" not found. '
+                               'Check target resid!'
+                               ''.format(_format_resname(resspec)))
 
 class AnnotateMutMod(Processor):
     """

diff --git a/vermouth/tests/test_annotate_mut_mod.py b/vermouth/tests/test_annotate_mut_mod.py
@@ -270,7 +270,7 @@ def test_annotate_mutmod_processor(example_mol, modifications, mutations, expect
         [(0, 1), (1, 2)],
         {1: ['N-ter'], 3: ['C-ter']}
     ),
-(
+    (
         [
             {'resname': 'XXX', 'resid': 1},
             {'resname': 'ALA', 'resid': 2},
@@ -289,7 +289,8 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
     mol = Molecule(force_field=ForceField(FF_UNIVERSAL_TEST))
     mol.add_nodes_from(enumerate(node_data))
     mol.add_edges_from(edge_data)
-    modification = [({'resname': 'cter'}, 'C-ter'), ({'resname': 'nter'}, 'N-ter')]
+    modification = [({'resname': 'cter'}, 'C-ter'), 
+                    ({'resname': 'nter'}, 'N-ter')]
 
     annotate_modifications(mol, modification, [])
 
@@ -300,3 +301,39 @@ def test_nter_cter_modifications(node_data, edge_data, expected):
             found[node['resid']] = node['modification']
 
     assert found == expected
+
+@pytest.mark.parametrize('node_data, edge_data, expected', [
+    (
+        [
+            {'resname': 'GLY', 'resid': 1},
+            {'resname': 'ALA', 'resid': 2},
+            {'resname': 'ALA', 'resid': 3}
+        ],
+        [(0, 1), (1, 2)],
+        False
+    ),
+    (
+        [
+            {'resname': 'ALA', 'resid': 1},
+            {'resname': 'ALA', 'resid': 2},
+            {'resname': 'ALA', 'resid': 3}
+        ],
+        [(0, 1), (1, 2)],
+        True
+    )])
+def test_mod_resid_not_correct(caplog, node_data, edge_data, expected):
+    """
+    Tests that the modification is found in the expected residue.
+    """
+    mol = Molecule(force_field=ForceField(FF_UNIVERSAL_TEST))
+    mol.add_nodes_from(enumerate(node_data))
+    mol.add_edges_from(edge_data)
+    mutation = [({'resname': 'GLY', 'resid': 1}, 'MET')]
+
+    caplog.clear()
+    annotate_modifications(mol, [], mutation)
+
+    if expected:        
+        assert '"GLY1" not found.' in str(caplog.records[0].getMessage())
+    else:
+        assert caplog.records == []