re-add old default

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

@@ -1957,40 +1957,37 @@ class PeriodicTorsionGenerator(object):
                 if type1 in types1:
                     for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
                         if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
-                            # topology atom indexes
-                            a2 = torsion[t2[1]]
-                            a3 = torsion[t3[1]]
-                            a4 = torsion[t4[1]]
-                            # residue indexes
-                            r2 = data.atoms[a2].residue.index
-                            r3 = data.atoms[a3].residue.index
-                            r4 = data.atoms[a4].residue.index
-                            # template atom indexes
-                            ta2 = data.atomTemplateIndexes[data.atoms[a2]]
-                            ta3 = data.atomTemplateIndexes[data.atoms[a3]]
-                            ta4 = data.atomTemplateIndexes[data.atoms[a4]]
-                            # elements
-                            e2 = data.atoms[a2].element
-                            e3 = data.atoms[a3].element
-                            e4 = data.atoms[a4].element
                             if tordef.ordering == 'default':
-                                    if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
-                                        (a2, a4) = (a4, a2)
-                                        r2 = data.atoms[a2].residue.index
-                                        r4 = data.atoms[a4].residue.index
-                                        ta2 = data.atomTemplateIndexes[data.atoms[a3]]
-                                        ta4 = data.atomTemplateIndexes[data.atoms[a4]]
-                                    if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
-                                        (a3, a4) = (a4, a3)
-                                        r3 = data.atoms[a3].residue.index
-                                        r4 = data.atoms[a4].residue.index
-                                        ta3 = data.atomTemplateIndexes[data.atoms[a3]]
-                                        ta4 = data.atomTemplateIndexes[data.atoms[a4]]
-                                    if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
-                                        (a2, a3) = (a3, a2)
-                                    elif hasTwoWildcards and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
-                                        (a2, a3) = (a3, a2)
+                                # Workaround to be more consistent with AMBER.  It uses wildcards to define most of its
+                                # impropers, which leaves the ordering ambiguous.  It then follows some bizarre rules
+                                # to pick the order.
+                                a1 = torsion[t2[1]]
+                                a2 = torsion[t3[1]]
+                                e1 = data.atoms[a1].element
+                                e2 = data.atoms[a2].element
+                                if e1 == e2 and a1 > a2:
+                                    (a1, a2) = (a2, a1)
+                                elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
+                                    (a1, a2) = (a2, a1)
+                                match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
+                                break
                             elif tordef.ordering == 'amber':
+                                # topology atom indexes
+                                a2 = torsion[t2[1]]
+                                a3 = torsion[t3[1]]
+                                a4 = torsion[t4[1]]
+                                # residue indexes
+                                r2 = data.atoms[a2].residue.index
+                                r3 = data.atoms[a3].residue.index
+                                r4 = data.atoms[a4].residue.index
+                                # template atom indexes
+                                ta2 = data.atomTemplateIndexes[data.atoms[a2]]
+                                ta3 = data.atomTemplateIndexes[data.atoms[a3]]
+                                ta4 = data.atomTemplateIndexes[data.atoms[a4]]
+                                # elements
+                                e2 = data.atoms[a2].element
+                                e3 = data.atoms[a3].element
+                                e4 = data.atoms[a4].element
                                 if not hasWildcard:
                                     if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
                                         (a2, a4) = (a4, a2)
@@ -2021,8 +2018,8 @@ class PeriodicTorsionGenerator(object):
                                         ta4 = data.atomTemplateIndexes[data.atoms[a4]]
                                     if r2 > r3 or (r2 == r3 and ta2 > ta3):
                                         (a2, a3) = (a3, a2)
-                            match = (a2, a3, torsion[0], a4, tordef)
-                            break
+                                match = (a2, a3, torsion[0], a4, tordef)
+                                break
             if match is not None:
                 (a1, a2, a3, a4, tordef) = match
                 for i in range(len(tordef.phase)):