Get rid of extra point element -- use "None" as no element

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

@@ -231,7 +231,11 @@ class CharmmParameterSet(object):
                     atomic_number = get_by_symbol(elem).atomic_number
                 except (IndexError, KeyError):
                     # Figure it out from the mass
-                    atomic_number = Element.getByMass(mass).atomic_number
+                    masselem = Element.getByMass(mass)
+                    if masselem is None:
+                        atomic_number = 0 # Extra point or something
+                    else:
+                        atomic_number = masselem.atomic_number
                 atype = AtomType(name=name, number=idx, mass=mass,
                                  atomic_number=atomic_number)
                 self.atom_types_str[atype.name] = atype
@@ -452,7 +456,11 @@ class CharmmParameterSet(object):
                 atomic_number = get_by_symbol(elem).atomic_number
             except (IndexError, KeyError):
                 # Figure it out from the mass
-                atomic_number = Element.getByMass(mass).atomic_number
+                masselem = Element.getByMass(mass)
+                if masselem is None:
+                    atomic_number = 0 # Extra point or something
+                else:
+                    atomic_number = masselem.atomic_number
             atype = AtomType(name=name, number=idx, mass=mass,
                              atomic_number=atomic_number)
             self.atom_types_str[atype.name] = atype

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

@@ -773,8 +773,12 @@ class CharmmPsfFile(object):
                 atomic_num = atom.type.atomic_number
                 elem = element.Element.getByAtomicNumber(atomic_num)
             else:
-                # If we didn't load a parameter set yet, try based on mass
-                elem = element.Element.getByMass(atom.mass)
+                # Figure it out from the mass
+                masselem = Element.getByMass(mass)
+                if masselem is None:
+                    atomic_number = 0 # Extra point or something
+                else:
+                    atomic_number = masselem.atomic_number
             topology.addAtom(atom.name, elem, residue)
 
         # Add all of the bonds

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

@@ -103,7 +103,7 @@ class Element(object):
         if not is_quantity(mass):
             mass = mass * daltons
         diff = mass
-        best_guess = Element._elements_by_atomic_number[0]
+        best_guess = None
 
         for key in Element._elements_by_atomic_number:
             element = Element._elements_by_atomic_number[key]
@@ -147,7 +147,6 @@ def _pickle_element(element):
 
 copy_reg.pickle(Element, _pickle_element)
 
-virtualsite =    Element(  0, "virtual site", "EP", 0.0*daltons)
 hydrogen =       Element(  1, "hydrogen", "H", 1.007947*daltons)
 deuterium =      Element(  1, "deuterium", "D", 2.01355321270*daltons)
 helium =         Element(  2, "helium", "He", 4.003*daltons)
@@ -270,5 +269,3 @@ ununhexium =     Element(116, "ununhexium",     "Uuh", 292*daltons)
 # relational operators will work with any chosen name
 sulphur = sulfur
 aluminium = aluminum
-extrapoint = virtualsite
-lonepair = virtualsite