GromacsTopFile supports [ settles ] directive (#4188)

wrappers/python/openmm/app/gromacstopfile.py

@@ -278,6 +278,8 @@ class GromacsTopFile(object):
                 self._processPair(line)
             elif self._currentCategory == 'constraints':
                 self._processConstraint(line)
+            elif self._currentCategory == 'settles':
+                self._processSettles(line)
             elif self._currentCategory == 'cmap':
                 self._processCmap(line)
             elif self._currentCategory == 'atomtypes':
@@ -411,6 +413,18 @@ class GromacsTopFile(object):
             raise ValueError('Too few fields in [ constraints ] line: '+line)
         self._currentMoleculeType.constraints.append(fields)
 
+    def _processSettles(self, line):
+        """Process a line in the [ settles ] category."""
+        if self._currentMoleculeType is None:
+            raise ValueError('Found [ settles ] section before [ moleculetype ]')
+        fields = line.split()
+        if len(fields) < 4:
+            raise ValueError('Too few fields in [ settles ] line: '+line)
+        atom = int(fields[0])
+        self._currentMoleculeType.constraints.append([str(atom), str(atom+1), fields[1], fields[2]])
+        self._currentMoleculeType.constraints.append([str(atom), str(atom+2), fields[1], fields[2]])
+        self._currentMoleculeType.constraints.append([str(atom+1), str(atom+2), fields[1], fields[3]])
+
     def _processCmap(self, line):
         """Process a line in the [ cmaps ] category."""
         if self._currentMoleculeType is None:

wrappers/python/tests/TestGromacsTopFile.py

@@ -218,6 +218,7 @@ class TestGromacsTopFile(unittest.TestCase):
         """Test a three particle virtual site."""
         top = GromacsTopFile('systems/tip4pew.top')
         system = top.createSystem()
+        self.assertEqual(3, system.getNumConstraints())
         self.assertTrue(system.isVirtualSite(3))
         vs = system.getVirtualSite(3)
         self.assertIsInstance(vs, ThreeParticleAverageSite)