Support initialization scripts in force fields (#3167)

wrappers/python/openmm/app/forcefield.py

@@ -330,7 +330,7 @@ class ForceField(object):
                             self.registerTemplatePatch(resName, patchName, 0)
                     self.registerResidueTemplate(template)
 
-        # Load the patch defintions.
+        # Load the patch definitions.
 
         for tree in trees:
             if tree.getroot().find('Patches') is not None:
@@ -411,6 +411,12 @@ class ForceField(object):
             for node in tree.getroot().findall('Script'):
                 self.registerScript(node.text)
 
+        # Execute initialization scripts.
+
+        for tree in trees:
+            for node in tree.getroot().findall('InitializationScript'):
+                exec(node.text, locals())
+
     def getGenerators(self):
         """Get the list of all registered generators."""
         return self._forces

wrappers/python/tests/TestForceField.py

@@ -1149,6 +1149,19 @@ END"""))
         self.assertAlmostEqual(26.10373, propers, delta=propers*1e-3) # DIHEdrals
         self.assertAlmostEqual(0.14113, impropers, delta=impropers*1e-3) # IMPRopers
 
+    def test_InitializationScript(self):
+        """Test that <InitializationScript> tags get executed."""
+        xml = """
+<ForceField>
+  <InitializationScript>
+self.scriptExecuted = True
+  </InitializationScript>
+</ForceField>
+"""
+        ff = ForceField(StringIO(xml))
+        self.assertTrue(ff.scriptExecuted)
+        
+
 class AmoebaTestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method with the AMOEBA forcefield."""