code: public void setExternalSelectedPart(IAtomContainer externalSelectedPart) {
          this.externalSelectedPart = externalSelectedPart;
          Map<IChemObject, Color> colorHash = getParameter(ColorHash.class).getValue();
          colorHash.clear();
          if (externalSelectedPart != null) {
              for (int i = 0; i < externalSelectedPart.getAtomCount(); i++) {
                  colorHash.put(externalSelectedPart.getAtom(i), getParameter(ExternalHighlightColor.class).getValue());
              }
              Iterator<IBond> bonds = externalSelectedPart.bonds().iterator();
              while (bonds.hasNext()) {
                  colorHash.put(bonds.next(), getParameter(ExternalHighlightColor.class).getValue());
              }
          }
          fireChange();
      }
docs: Set externally selected atoms. These are atoms selected externally in e.
  g. Bioclipse via the ChemObjectTree, painted in externalSelectedPartColor
  
  @param externalSelectedPart
  the selected part