code: protected static IAtomContainer makeAtomContainer(IAtom atom, List<IBond> parts, IAtom excludedAtom) {
          IAtomContainer partContainer = atom.getBuilder().newInstance(IAtomContainer.class);
          partContainer.addAtom(atom);
          for (IBond aBond : parts) {
              for (IAtom bondedAtom : aBond.atoms()) {
                  if (!bondedAtom.equals(excludedAtom) && !partContainer.contains(bondedAtom))
                      partContainer.addAtom(bondedAtom);
              }
              if (!aBond.contains(excludedAtom)) partContainer.addBond(aBond);
          }
          return partContainer;
      }
docs: splitting bond itself