code: public static double getRadius(Atom atom) {
  
  		if (atom.getElement()==null) {
  			logger.warn("Unrecognised atom "+atom.getName()+" with serial "+atom.getPDBserial()+
  					", assigning the default vdw radius (Nitrogen vdw radius).");
  			return Element.N.getVDWRadius();
  		}
  
  		Group res = atom.getGroup();
  
  		if (res==null) {
  			logger.warn("Unknown parent residue for atom "+atom.getName()+" with serial "+
  					atom.getPDBserial()+", assigning its default vdw radius");
  			return atom.getElement().getVDWRadius();
  		}
  
  		GroupType type = res.getType();
  
  		if (type == GroupType.AMINOACID) return getRadiusForAmino(((AminoAcid)res), atom);
  
  		if (type == GroupType.NUCLEOTIDE) return getRadiusForNucl((NucleotideImpl)res,atom);
  
  
  		return atom.getElement().getVDWRadius();
  	}
docs: Gets the van der Waals radius of the given atom following the values defined by
  Chothia (1976) J.Mol.Biol.105,1-14
  NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates"
  slightly the heavy atoms to account for Hydrogens. Thus this method cannot be used
  in a structure that contains Hydrogens!
  
  If atom is neither part of a nucleotide nor of a standard aminoacid,
  the default vdw radius for the element is returned. If atom is of
  unknown type (element) the vdw radius of {@link Element().N} is returned
  
  @param atom
  @return