code: @Override
  	public String getAtomSequence(){
  
  
  		List<Group> groups = getAtomGroups();
  		StringBuilder sequence = new StringBuilder() ;
  
  		for ( Group g: groups){
  			ChemComp cc = g.getChemComp();
  
  			if ( PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
  					PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())){
  				// an amino acid residue.. use for alignment
  				String oneLetter= ChemCompGroupFactory.getOneLetterCode(cc);
  				if ( oneLetter == null)
  					oneLetter = Character.toString(StructureTools.UNKNOWN_GROUP_LABEL);
  				sequence.append(oneLetter);
  			}
  
  		}
  		return sequence.toString();
  
  
  	}
docs: {@inheritDoc}