added Forcefield.apply assert_bonds

foyer/forcefield.py

@@ -340,8 +340,9 @@ def registerAtomType(self, parameters):
             self.atomTypeRefs[name] = dois
 
     def apply(self, topology, references_file=None, use_residue_map=True,
-              assert_angle_params=True, assert_dihedral_params=True,
-              assert_improper_params=False, *args, **kwargs):
+              assert_bond_params=True, assert_angle_params=True,
+              assert_dihedral_params=True, assert_improper_params=False,
+              *args, **kwargs):
         """Apply the force field to a molecular structure
 
         Parameters
@@ -360,6 +361,9 @@ def apply(self, topology, references_file=None, use_residue_map=True,
             residues, i.e. a box of water. Note that for this to be applied to
             independent molecules, they must each be saved as different
             residues in the topology.
+        assert_bond_params : bool, optional, default=True
+            If True, Foyer will exit if parameters are not found for all system
+            bonds.
         assert_angle_params : bool, optional, default=True
             If True, Foyer will exit if parameters are not found for all system
             angles.
@@ -390,6 +394,16 @@ def apply(self, topology, references_file=None, use_residue_map=True,
         '''
         data = self._SystemData
 
+        if data.bonds:
+            missing = [b for b in structure.bonds
+                       if b.type is None]
+            if missing:
+                nmissing = len(structure.bonds) - len(missing)
+                msg = ("Parameters have not been assigned to all bonds. "
+                       "Total system bonds: {}, Parametrized bonds: {}"
+                       "".format(len(structure.bonds), nmissing))
+                _error_or_warn(assert_bond_params, msg)
+
         if data.angles and (len(data.angles) != len(structure.angles)):
             msg = ("Parameters have not been assigned to all angles. Total "
                    "system angles: {}, Parameterized angles: {}"

foyer/tests/test_forcefield.py

@@ -206,3 +206,20 @@ def test_overrides_space():
     ff = Forcefield(forcefield_files=get_fn('overrides-space.xml'))
     typed_ethane = ff.apply(ethane)
     assert typed_ethane.atoms[0].type == 'CT3'
+
+def test_assert_bonds():
+    ff = Forcefield(name='trappe-ua')
+
+    derponium = mb.Compound()
+    at1 = mb.Particle(name='H')
+    at2 = mb.Particle(name='O')
+    at3 = mb.Particle(name='_CH4')
+
+    derponium.add([at1, at2, at3])
+    derponium.add_bond((at1, at2))
+    derponium.add_bond((at2, at3))
+
+    with pytest.raises(Exception):
+        ff.apply(derponium)
+    thing = ff.apply(derponium, assert_bond_params=False, assert_angle_params=False)
+    assert any(b.type is None for b in thing.bonds)