Fix position of existing atoms on addHydrogens()

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

@@ -712,6 +712,8 @@ class Modeller(object):
         automatically, this function will only add hydrogens.  It will never remove ones that are already present in the
         model, regardless of the specified pH.
 
+        In all cases, the positions of existing atoms (including existing hydrogens) are not modified.
+
         Definitions for standard amino acids and nucleotides are built in.  You can call loadHydrogenDefinitions() to load
         additional definitions for other residue types.
 
@@ -930,14 +932,16 @@ class Modeller(object):
 
         # The hydrogens were added at random positions.  Now perform an energy minimization to fix them up.
 
+        addedH = set(newIndices)  # keep track of Hs added
+
         if forcefield is not None:
             # Use the ForceField the user specified.
 
             system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic)
             atoms = list(newTopology.atoms())
             for i in range(system.getNumParticles()):
-                if atoms[i].element != elem.hydrogen:
-                    # This is a heavy atom, so make it immobile.
+                if i not in addedH:
+                    # Existing atom, make it immobile.
                     system.setParticleMass(i, 0)
         else:
             # Create a System that restrains the distance of each hydrogen from its parent atom
@@ -955,7 +959,7 @@ class Modeller(object):
             bondedTo = []
             for atom in newTopology.atoms():
                 nonbonded.addParticle([])
-                if atom.element != elem.hydrogen:
+                if atom.index not in addedH:  # make immobile
                     system.addParticle(0.0)
                 else:
                     system.addParticle(1.0)