code: private boolean hasFixedPart(final IAtomContainer mol) {
          if (afix.isEmpty()) return false;
          for (IAtom atom : mol.atoms())
              if (afix.contains(atom))
                  return true;
          return false;
      }
docs: Determine if any atoms in a connected molecule are fixed (i.e. already have coordinates/
  have been placed).
  
  @param mol the moleucle to check
  @return atoms are fixed