Merge pull request #842 from peastman/residue

Fixed exception in addExtraParticles()

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

@@ -924,7 +924,7 @@ class Modeller(object):
                     # extra points.
 
                     template = None
-                    residueNoEP = Residue(residue.name, residue.index, residue.chain)
+                    residueNoEP = Residue(residue.name, residue.index, residue.chain, residue.id)
                     residueNoEP._atoms = [atom for atom in residue.atoms() if atom.element is not None]
                     if signature in forcefield._templateSignatures:
                         for t in forcefield._templateSignatures[signature]:

wrappers/python/tests/TestModeller.py

@@ -886,6 +886,27 @@ class TestModeller(unittest.TestCase):
 
         validate_equivalence(self, topology_LYN, topology_after)
 
+
+    def test_addExtraParticles(self):
+        """Test addExtraParticles()."""
+
+        # Create a box of water.
+
+        ff1 = ForceField('tip3p.xml')
+        modeller = Modeller(Topology(), []*nanometers)
+        modeller.addSolvent(ff1, 'tip3p', boxSize=Vec3(2,2,2)*nanometers)
+
+        # Now convert the water to TIP4P.
+
+        ff2 = ForceField('tip4pew.xml')
+        modeller.addExtraParticles(ff2)
+        for residue in modeller.topology.residues():
+            atoms = list(residue.atoms())
+            self.assertEqual(4, len(atoms))
+            ep = [atom for atom in atoms if atom.element is None]
+            self.assertEqual(1, len(ep))
+
+
     def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
         scale = max(1.0, norm(p1),)
         for i in range(3):