Personal commit to make modeller easier to use

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

@@ -734,9 +734,8 @@ class Modeller(object):
                                     else:
                                         delta = Vec3(random.random(), random.random(), random.random())*nanometer
                                     delta *= 0.1*nanometer/norm(delta)
-                                    if len(expected) > 1:
-                                        delta += 0.05*Vec3(random.random(), random.random(), random.random())*nanometer
-                                        delta *= 0.1*nanometer/norm(delta)
+                                    delta += 0.05*Vec3(random.random(), random.random(), random.random())*nanometer
+                                    delta *= 0.1*nanometer/norm(delta)
                                     newPositions.append(self.positions[parent.index]+delta)
                                     newTopology.addBond(newAtom, newH)
                 else:
@@ -758,7 +757,9 @@ class Modeller(object):
             if atoms[i].element != elem.hydrogen:
                 # This is a heavy atom, so make it immobile.
                 system.setParticleMass(i, 0)
-        context = Context(system, VerletIntegrator(0.0))
+        from simtk.openmm import Platform
+        plt = Platform.getPlatformByName('Reference')
+        context = Context(system, VerletIntegrator(0.0), plt)
         context.setPositions(newPositions)
         LocalEnergyMinimizer.minimize(context)
         self.topology = newTopology
@@ -922,4 +923,4 @@ class Modeller(object):
             if bond[0] in newAtoms and bond[1] in newAtoms:
                 newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
         self.topology = newTopology
-        self.positions = newPositions
+        self.positions = newPositions
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