code: private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
  
  		if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
  		if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
  
  		if (atom.getElement()==Element.C) return NUC_CARBON_VDW;
  
  		if (atom.getElement()==Element.N) return NUC_NITROGEN_VDW;
  
  		if (atom.getElement()==Element.P) return PHOSPHOROUS_VDW;
  
  		if (atom.getElement()==Element.O) return OXIGEN_VDW;
  
  		logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius");
  		return atom.getElement().getVDWRadius();
  	}
docs: Gets the radius for given nucleotide atom
  @param atom
  @return