code: @Override
  	public void setAtoms(List<Atom> atoms) {
  
  		// important we are resetting atoms to a new list, we need to reset the lookup too!
  		if ( atomNameLookup != null)
  			atomNameLookup.clear();
  
  		for (Atom a: atoms){
  			a.setGroup(this);
  			if ( atomNameLookup != null)
  				atomNameLookup.put(a.getName(),a);
  		}
  		this.atoms = atoms;
  		if (!atoms.isEmpty()) {
  			pdb_flag = true;
  		}
  
  	}
docs: {@inheritDoc}