code: public static IAtomContainer project(List<CDKRMap> rMapList, IAtomContainer graph, int key) {
          IAtomContainer atomContainer = graph.getBuilder().newInstance(IAtomContainer.class);
  
          Map<IAtom, IAtom> table = new HashMap<IAtom, IAtom>();
          IAtom atom1;
          IAtom atom2;
          IAtom atom;
          IBond bond;
  
          for (Iterator<CDKRMap> i = rMapList.iterator(); i.hasNext();) {
              CDKRMap rMap = i.next();
              if (key == CDKMCS.ID1) {
                  bond = graph.getBond(rMap.getId1());
              } else {
                  bond = graph.getBond(rMap.getId2());
              }
  
              atom = bond.getBegin();
              atom1 = table.get(atom);
  
              if (atom1 == null) {
                  try {
                      atom1 = (IAtom) atom.clone();
                  } catch (CloneNotSupportedException e) {
                      e.printStackTrace();
                  }
                  atomContainer.addAtom(atom1);
                  table.put(atom, atom1);
              }
  
              atom = bond.getEnd();
              atom2 = table.get(atom);
  
              if (atom2 == null) {
                  try {
                      atom2 = (IAtom) atom.clone();
                  } catch (CloneNotSupportedException e) {
                      e.printStackTrace();
                  }
                  atomContainer.addAtom(atom2);
                  table.put(atom, atom2);
              }
              IBond newBond = graph.getBuilder().newInstance(IBond.class, atom1, atom2, bond.getOrder());
              newBond.setFlag(CDKConstants.ISAROMATIC, bond.getFlag(CDKConstants.ISAROMATIC));
              atomContainer.addBond(newBond);
          }
          return atomContainer;
      }
docs: Projects atom list of CDKRMap on atom molecule.
  
  @param  rMapList  the list to project
  @param  graph         the molecule on which project
  @param  key        the key in the CDKRMap of the molecule graph
  @return           an AtomContainer