Added an argument to addHydrogens() for selecting which Platform to use for...

Added an argument to addHydrogens() for selecting which Platform to use for minimization.  Also marked convertWater() as deprecated.

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

@@ -176,6 +176,8 @@ class Modeller(object):
 
         Parameters:
          - model (string='tip3p') the water model to convert to.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
+        
+        @deprecated Use addExtraParticles() instead.  It performs the same function but in a more general way.
         """
         if model in ('tip3p', 'spce'):
             sites = 3
@@ -517,7 +519,7 @@ class Modeller(object):
                     terminal = hydrogen.attrib['terminal']
                 data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))
 
-    def addHydrogens(self, forcefield, pH=7.0, variants=None):
+    def addHydrogens(self, forcefield, pH=7.0, variants=None, platform=None):
         """Add missing hydrogens to the model.
 
         Some residues can exist in multiple forms depending on the pH and properties of the local environment.  These
@@ -564,6 +566,8 @@ class Modeller(object):
          - variants (list=None) an optional list of variants to use.  If this is specified, its length must equal the number
            of residues in the model.  variants[i] is the name of the variant to use for residue i (indexed starting at 0).
            If an element is None, the standard rules will be followed to select a variant for that residue.
+         - platform (Platform=None) the Platform to use when computing the hydrogen atom positions.  If this is None,
+           the default Platform will be used.
         Returns: a list of what variant was actually selected for each residue, in the same format as the variants parameter
         """
         # Check the list of variants.
@@ -757,7 +761,10 @@ 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))
+        if platform is None:
+            context = Context(system, VerletIntegrator(0.0))
+        else:
+            context = Context(system, VerletIntegrator(0.0), platform)
         context.setPositions(newPositions)
         LocalEnergyMinimizer.minimize(context)
         self.topology = newTopology