PartialBondHighlight.java

public class Main {
  public static void main(String[] args) throws CDKException, IOException {

    String smi = "C1[C@H]([C@@H](OC2=CC(=CC(=C21)O)O)*)O |$;;;;;;;;;;;;_AP1$|";
    SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
    IAtomContainer mol = smipar.parseSmiles(smi);

    // atom indexes to highlight
    int[] idxs = new int[]{3,4,5,9};
    boolean outgoing = true;

    Set<IAtom> atomHighlight = new HashSet<>();
    Set<IBond> bondHighlight = new HashSet<>();
    Set<IAtom> atomMask = new HashSet<>();

    for (int idx : idxs)
      atomHighlight.add(mol.getAtom(idx));
    for (IAtom atom : atomHighlight) {
      if (outgoing) {
        bondHighlight.addAll(mol.getConnectedBondsList(atom));
      } else {
        for (IBond bond : mol.getConnectedBondsList(atom)) {
          if (atomHighlight.contains(bond.getConnectedAtom(atom)))
            bondHighlight.add(bond);
        }
      }
    }
    if (outgoing) {
      for (IBond bond : bondHighlight) {
        IAtom beg = bond.getAtom(0);
        IAtom end = bond.getAtom(1);
        if (!atomHighlight.contains(beg))
          atomMask.add(beg);
        if (!atomHighlight.contains(end))
          atomMask.add(end);
      }
    }

    DepictionGenerator dg = new DepictionGenerator();
    dg = dg.withSize(250, 250);
    dg = dg.withOuterGlowHighlight();
    dg = dg.withHighlight(atomHighlight, new Color(0xff9999))
           .withHighlight(bondHighlight, new Color(0xff9999))
           .withHighlight(atomMask, Color.WHITE);
    dg.depict(mol).writeTo("~/tmp.png");
  }
}