Merge pull request #1785 from peastman/include

ForceFields can include other files

docs-source/usersguide/application.rst

@@ -2937,6 +2937,32 @@ need to be specified once for each class.  The atom charges, which are different
 for each type, are taken from the residue template instead.
 
 
+Including Other Files
+=====================
+
+Sometimes it is useful to split a force field definition into multiple files,
+but still be able to use the force field by specifying only a single file.  You
+can accomplish this with the :code:`<Include>` tag.  For example:
+
+.. code-block:: xml
+
+    <ForceField>
+     <Include file="definitions.xml"/>
+     ...
+    </ForceField>
+
+The :code:`file` attribute gives the path of the file to include.  It may be
+relative either to the directory containing the parent XML file (the one with
+the :code:`<Include>` tag) or the OpenMM data directory (the one containing
+built in force fields).
+
+The included file is fully processed before any other tags in the parent file
+are processed, and its definitions are added to the force field.  This means the
+parent file can refer to atom types defined in the included file, but not the
+other way around.  If there are multiple :code:`<Include>` tags, they are processed
+in the order they appear in the file.
+
+
 Using Multiple Files
 ********************
 

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

@@ -205,6 +205,19 @@ class ForceField(object):
 
             trees.append(tree)
 
+        # Process includes.
+        
+        for parentFile, tree in zip(files, trees):
+            if isinstance(parentFile, str):
+                parentDir = os.path.dirname(parentFile)
+            else:
+                parentDir = ''
+            for include in tree.getroot().findall('Include'):
+                includeFile = include.attrib['file']
+                joined = os.path.join(parentDir, includeFile)
+                if os.path.isfile(joined):
+                    includeFile = joined
+                self.loadFile(includeFile)
 
         # Load the atom types.
 

wrappers/python/tests/TestForceField.py

@@ -762,6 +762,13 @@ class TestForceField(unittest.TestCase):
         self.assertEqual('ALA', templates[0].name)
         self.assertEqual('NME', templates[1].name)
 
+    def test_Includes(self):
+        """Test using a ForceField that includes other files."""
+        forcefield = ForceField(os.path.join('systems', 'ff_with_includes.xml'))
+        self.assertTrue(len(forcefield._atomTypes) > 10)
+        self.assertTrue('spce-O' in forcefield._atomTypes)
+        self.assertTrue('HOH' in forcefield._templates)
+
 
 class AmoebaTestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method with the AMOEBA forcefield."""

wrappers/python/tests/systems/ff_with_includes.xml

+<ForceField>
+    <Include file="test_amber_ff.xml"/>
+    <Include file="spce.xml"/>
+</ForceField>
\ No newline at end of file