Merge pull request #2269 from tristanic/master

Avoid repeated matching of duplicate impropers

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

@@ -1968,12 +1968,15 @@ class PeriodicTorsionGenerator(object):
         else:
             force = existing[0]
         wildcard = self.ff._atomClasses['']
+        proper_cache = {}
         for torsion in data.propers:
-            type1 = data.atomType[data.atoms[torsion[0]]]
-            type2 = data.atomType[data.atoms[torsion[1]]]
-            type3 = data.atomType[data.atoms[torsion[2]]]
-            type4 = data.atomType[data.atoms[torsion[3]]]
-            match = None
+            type1, type2, type3, type4 = [data.atomType[data.atoms[torsion[i]]] for i in range(4)]
+            sig = (type1, type2, type3, type4)
+            sig = frozenset((sig, sig[::-1]))
+            match = proper_cache.get(sig, None)
+            if match == -1:
+                continue
+            if match is None:
                 for index in self.propersForAtomType[type2]:
                     tordef = self.proper[index]
                     types1 = tordef.types1
@@ -1986,18 +1989,39 @@ class PeriodicTorsionGenerator(object):
                             match = tordef
                         if not hasWildcard:
                             break
+                if match is None:
+                    proper_cache[sig] = -1
+                else:
+                    proper_cache[sig] = match
             if match is not None:
                 for i in range(len(match.phase)):
                     if match.k[i] != 0:
                         force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], match.periodicity[i], match.phase[i], match.k[i])
+        impr_cache = {}
         for torsion in data.impropers:
+            t1, t2, t3, t4 = tatoms = [data.atomType[data.atoms[torsion[i]]] for i in range(4)]
+            sig = (t1, t2, t3, t4)
+            match = impr_cache.get(sig, None)
+            if match == -1:
+                # Previously checked, and doesn't appear in the database
+                continue
+            elif match:
+                i1, i2, i3, i4, tordef = match
+                a1, a2, a3, a4 = (torsion[i] for i in (i1, i2, i3, i4))
+                match = (a1, a2, a3, a4, tordef)
+            if match is None:
                 match = _matchImproper(data, torsion, self)
+                if match is not None:
+                    order = match[:4]
+                    i1, i2, i3, i4 = tuple(torsion.index(a) for a in order)
+                    impr_cache[sig] = (i1, i2, i3, i4, match[-1])
+                else:
+                    impr_cache[sig] = -1
             if match is not None:
                 (a1, a2, a3, a4, tordef) = match
                 for i in range(len(tordef.phase)):
                     if tordef.k[i] != 0:
                         force.addTorsion(a1, a2, a3, a4, tordef.periodicity[i], tordef.phase[i], tordef.k[i])
-
 parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement