code: public void assignVdWRadiiToProtein() {
          AtomTypeFactory atf = null;
          IAtom[] atoms = AtomContainerManipulator.getAtomArray(protein);
          try {
              atf = AtomTypeFactory.getInstance(vanDerWaalsFile, atoms[0].getBuilder());
          } catch (Exception ex1) {
              System.out.println("Problem with AtomTypeFactory due to:" + ex1.toString());
          }
          for (int i = 0; i < atoms.length; i++) {
              try {
                  atf.configure(atoms[i]);
              } catch (Exception ex2) {
                  logger.error("Problem with atf.configure due to:" + ex2.toString());
              }
          }
  
      }
docs: Method which assigns van der Waals radii to the biopolymer
  default org/openscience/cdk/config/data/pdb_atomtypes.xml
  stored in the variable String vanDerWaalsFile.