‌

Working with Bonds

Once again we can define many functions on our Bond , but for now we can just define the following:

Options[DisplayBond]=Flatten@{
 Options@DisplayAtom,
 BondWidth->Automatic
 };
DisplayBond[b_Bond,ops:OptionsPattern[]]:=Graphics3D[
 With[{p1=b["Atom1"]["Position"],
   p2=b["Atom2"]["Position"],
   v=b["Atom2"]["Position"]-b["Atom1"]["Position"],
   bw=Replace[OptionValue@BondWidth,Except[_?NumericQ]:>.1]},
  {EdgeForm[None],
   {b["Atom1"]["Color"],Cylinder[{p1,p1+1/2Norm@v*Normalize@v},bw]},
   {b["Atom2"]["Color"],Cylinder[{p2,p2-1/2Norm@v*Normalize@v},bw]}
   }],FilterRules[{ops,
   Options@DisplayBond
   },
  Options@Graphics3D]
 ]