Merge pull request #2464 from peastman/element

Improved determination of elements from Gromacs top files

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

@@ -563,8 +563,11 @@ class GromacsTopFile(object):
                     if atomName in atomReplacements:
                         atomName = atomReplacements[atomName]
 
-                    # Try to guess the element.
+                    # Try to determine the element.
 
+                    atomicNumber = self._atomTypes[fields[1]][2]
+                    if atomicNumber is None:
+                        # Try to guess the element from the name.
                         upper = atomName.upper()
                         if upper.startswith('CL'):
                             element = elem.chlorine
@@ -577,6 +580,10 @@ class GromacsTopFile(object):
                                 element = elem.get_by_symbol(atomName[0])
                             except KeyError:
                                 element = None
+                    elif atomicNumber == '0':
+                        element = None
+                    else:
+                        element = elem.Element.getByAtomicNumber(int(atomicNumber))
                     atoms.append(top.addAtom(atomName, element, r))
 
                 # Add bonds to the topology

wrappers/python/tests/TestGromacsTopFile.py

@@ -172,6 +172,13 @@ class TestGromacsTopFile(unittest.TestCase):
 
         top = GromacsTopFile('systems/bnz.top')
         gro = GromacsGroFile('systems/bnz.gro')
+        for atom in top.topology.atoms():
+            if atom.name.startswith('C'):
+                self.assertEqual(elem.carbon, atom.element)
+            elif atom.name.startswith('H'):
+                self.assertEqual(elem.hydrogen, atom.element)
+            else:
+                self.assertIsNone(atom.element)
         system = top.createSystem()
 
         self.assertEqual(26, system.getNumParticles())