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Making an Atom

To make an atom we start out by simply making an association to hold the properties of the atom and wrapping the Head Atom around it:

SetChemicalSystemUpValues@Atom;

elementDict[el_]:=<|
 "Position"->{0,0,0},
 "Mass"->ElementData[el,"AtomicMass"],
 "Radius"->ElementData[el,"VanDerWaalsRadius"],
 "Bonds"->{},
 "Valence"->ElementData[el,"Valence"],
 "Color"->ColorData["Atoms"][el]
 |>;
 Atom[attrs:(_Rule|_RuleDelayed)..]:=ChemicalSystemAdd[
  Atom@With[{ad=<|attrs|>},
    Replace[ad["Element"],{
      e_String:>Merge[{ad,elementDict[e]},First],
      _->$Failed}]
    ]];
   Atom[element_String,
    position:{x_?NumericQ,y_?NumericQ,z_?NumericQ}:Automatic,
    mass:_?NumericQ:Automatic
    ]:=Atom@@DeleteCases[{"Element"->element,"Position"->position,"Mass"->mass},_->Automatic]