code: public static IAtomContainer createNewMolecule(IChemModel chemModel) {
          // Add a new molecule either the set of molecules
          IAtomContainer molecule = chemModel.getBuilder().newInstance(IAtomContainer.class);
          if (chemModel.getMoleculeSet() != null) {
              IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
              for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++) {
                  if (moleculeSet.getAtomContainer(i).getAtomCount() == 0) {
                      moleculeSet.removeAtomContainer(i);
                      i--;
                  }
              }
              moleculeSet.addAtomContainer(molecule);
          } else {
              IAtomContainerSet moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
              moleculeSet.addAtomContainer(molecule);
              chemModel.setMoleculeSet(moleculeSet);
          }
          return molecule;
      }
docs: Adds a new Molecule to the MoleculeSet inside a given ChemModel.
  Creates a MoleculeSet if none is contained.
  
  @param chemModel  The ChemModel object.
  @return           The created Molecule object.