Merge pull request #166 from marrink-lab/test-molecule-layout

Bring the formatting of test_molecule in line with the rest
marrink-lab · Jan 19, 2019 · 3af8756 · 3af8756
2 parents 7ee3771 + 5deed6a
commit 3af8756
Showing 1 changed file with 71 additions and 41 deletions.
diff --git a/vermouth/tests/test_molecule.py b/vermouth/tests/test_molecule.py
@@ -48,43 +48,62 @@ def molecule_copy(molecule):
 
 
 @pytest.mark.parametrize('atoms, bonds, interactions, removed, expected', [
-
     # empty molecule
     ([], [], [], [], {}),
-
     # Nodes but no interactions
     ([1, 2, 3], [(1, 2), (2, 3)], [], [2], {}),
-
     # interactions that all need to be removed
     ([1, 2], [(1, 2)], [('bond', (1, 2), {})], [2], {}),
-
     # Molecule with interactions of which some need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7)], [('bond', (5, 4), {}), ('bond', (1, 2), {})], [5]
-     , {'bond': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7)],
+        [('bond', (5, 4), {}), ('bond', (1, 2), {})],
+        [5],
+        {'bond': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}
+    ),
     # Molecule with interactions of which none need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4)], [('bond', (5, 4), {}), ('bond', (1, 2), {})], [6, 7]
-     , {'bond': [vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={})
-                 , vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4)],
+        [('bond', (5, 4), {}), ('bond', (1, 2), {})],
+        [6, 7],
+        {'bond': [vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={}),
+                  vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}
+    ),
     # Molecule with interactions of different types of which all need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7), (6, 7)], [('bond', (1, 6), {}), ('bond', (5, 4), {})
-                                                               , ('angle', (1, 2), {})], [1, 5], {}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7), (6, 7)],
+        [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})],
+        [1, 5],
+        {}
+    ),
     # Molecule with interactions of different types of which some need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7), (6, 7)]
-     , [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})], [5]
-     , {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]
-                 , 'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})]}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7), (6, 7)],
+        [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})],
+        [5],
+        {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
+         'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})]}
+    ),
     # Molecule with interactions of different types of which none need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7), (6, 7)]
-     , [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})], [3]
-     , {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]
-                 , 'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})
-                            , vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={})]}),
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7), (6, 7)],
+        [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})],
+        [3],
+        {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
+         'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={}),
+                  vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={})]}
+    ),
 ])
 def test_remove_nodes_from(atoms, bonds, interactions, removed, expected):
+    """
+    Test whether molecule.remove_nodes_from also removes the corresponding
+    interactions
+    """
     molecule = vermouth.molecule.Molecule()
     molecule.add_nodes_from(atoms)
     molecule.add_edges_from(bonds)
@@ -96,34 +115,45 @@ def test_remove_nodes_from(atoms, bonds, interactions, removed, expected):
 
 
 @pytest.mark.parametrize('atoms, bonds, interactions, removed, expected', [
-
     # empty molecule
     ([], [], [], None, {}),
-
     # Nodes but no interactions
     ([1, 2, 3], [(1, 2), (2, 3)], [], 2, {}),
-
     # interactions that all need to be removed
     ([1, 2], [(1, 2)], [('bond', (1, 2), {})], 2, {}),
-
     # Molecule with interactions of which some need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7)], [('bond', (5, 4), {}), ('bond', (1, 2), {})], 5
-     , {'bond': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7)],
+        [('bond', (5, 4), {}), ('bond', (1, 2), {})],
+        5,
+        {'bond': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})]}
+    ),
     # Molecule with interactions of different types of which some need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7), (6, 7)]
-     , [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})], 5
-     , {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
-        'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})]}),
-
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7), (6, 7)],
+        [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})],
+        5,
+        {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
+         'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})]}
+    ),
     # Molecule with interactions of different types of which none need to be removed
-    ([1, 2, 3, 4, 5, 6, 7], [(1, 2), (3, 4), (5, 7), (6, 7)]
-     , [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})], 3
-     , {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
-        'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={})
-                 , vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={})]}),
+    (
+        [1, 2, 3, 4, 5, 6, 7],
+        [(1, 2), (3, 4), (5, 7), (6, 7)],
+        [('bond', (1, 6), {}), ('bond', (5, 4), {}), ('angle', (1, 2), {})],
+        3,
+        {'angle': [vermouth.molecule.Interaction(atoms=(1, 2), meta={}, parameters={})],
+         'bond': [vermouth.molecule.Interaction(atoms=(1, 6), meta={}, parameters={}),
+                  vermouth.molecule.Interaction(atoms=(5, 4), meta={}, parameters={})]}
+    ),
 ])
 def test_remove_node(atoms, bonds, interactions, removed, expected):
+    """
+    Test whether molecule.remove_node also removes the corresponding
+    interactions
+    """
     molecule = vermouth.molecule.Molecule()
     molecule.add_nodes_from(atoms)
     molecule.add_edges_from(bonds)