code: public static IChemModel newChemModel(IAtomContainer atomContainer) {
          IChemModel model = atomContainer.getBuilder().newInstance(IChemModel.class);
          IAtomContainerSet moleculeSet = model.getBuilder().newInstance(IAtomContainerSet.class);
          moleculeSet.addAtomContainer(atomContainer);
          model.setMoleculeSet(moleculeSet);
          return model;
      }
docs: Create a new ChemModel containing an IAtomContainer. It will create an
  {@link IAtomContainer} from the passed IAtomContainer when needed, which may cause
  information loss.
  
  @param  atomContainer  The AtomContainer to have inside the ChemModel.
  @return                The new IChemModel object.