Merge pull request #1348 from rafwiewiora/forcefield_type_wildcard

Enable wildcard use for Atom Types

wrappers/python/simtk/openmm/app/forcefield.py

@@ -320,11 +320,15 @@ class ForceField(object):
                     types.append(None) # Unknown atom class
                 else:
                     types.append(self._atomClasses[attrib[classAttrib]])
-            else:
-                if typeAttrib not in attrib or attrib[typeAttrib] not in self._atomTypes:
+            elif typeAttrib in attrib:
+                if attrib[typeAttrib] == '':
+                    types.append(self._atomClasses[''])
+                elif attrib[typeAttrib] not in self._atomTypes:
                     types.append(None) # Unknown atom type
                 else:
                     types.append([attrib[typeAttrib]])
+            else:
+                types.append(None) # Unknown atom type
         return types
 
     def _parseTorsion(self, attrib):

wrappers/python/tests/TestForceField.py

@@ -434,6 +434,45 @@ class AmoebaTestForceField(unittest.TestCase):
             diff = norm(f1-f2)
             self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
 
+    def test_Wildcard(self):
+        """Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in the ffxml are correctly registered"""
+
+        # Use wildcards in types
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="C" class="C" element="C" mass="12.010000"/>
+  <Type name="O" class="O" element="O" mass="16.000000"/>
+ </AtomTypes>
+ <PeriodicTorsionForce>
+  <Proper type1="" type2="C" type3="C" type4="" periodicity1="2" phase1="3.141593" k1="15.167000"/>
+  <Improper type1="C" type2="" type3="" type4="O" periodicity1="2" phase1="3.141593" k1="43.932000"/>
+ </PeriodicTorsionForce>
+</ForceField>"""
+
+        ff = ForceField(StringIO(xml))
+
+        self.assertEqual(len(ff._forces[0].proper), 1)
+        self.assertEqual(len(ff._forces[0].improper), 1)
+
+       # Use wildcards in classes
+        xml = """
+<ForceField>
+ <AtomTypes>
+  <Type name="C" class="C" element="C" mass="12.010000"/>
+  <Type name="O" class="O" element="O" mass="16.000000"/>
+ </AtomTypes>
+ <PeriodicTorsionForce>
+  <Proper class1="" class2="C" class3="C" class4="" periodicity1="2" phase1="3.141593" k1="15.167000"/>
+  <Improper class1="C" class2="" class3="" class4="O" periodicity1="2" phase1="3.141593" k1="43.932000"/>
+ </PeriodicTorsionForce>
+</ForceField>"""
+
+        ff = ForceField(StringIO(xml))
+
+        self.assertEqual(len(ff._forces[0].proper), 1)
+        self.assertEqual(len(ff._forces[0].improper), 1)
+
 if __name__ == '__main__':
     unittest.main()