code: private Atom convertAtom(AtomSite atom){
  
  
  		Atom a = new AtomImpl();
  
  		a.setPDBserial(Integer.parseInt(atom.getId()));
  		a.setName(atom.getLabel_atom_id());
  
  		double x = Double.parseDouble (atom.getCartn_x());
  		double y = Double.parseDouble (atom.getCartn_y());
  		double z = Double.parseDouble (atom.getCartn_z());
  		a.setX(x);
  		a.setY(y);
  		a.setZ(z);
  
  		float occupancy = Float.parseFloat (atom.getOccupancy());
  		a.setOccupancy(occupancy);
  
  		float temp = Float.parseFloat (atom.getB_iso_or_equiv());
  		a.setTempFactor(temp);
  
  		String alt = atom.getLabel_alt_id();
  		if (( alt != null ) && ( alt.length() > 0) && (! alt.equals("."))){
  			a.setAltLoc(new Character(alt.charAt(0)));
  		} else {
  			a.setAltLoc(new Character(' '));
  		}
  
  		Element element = Element.R;
  		try {
  			element = Element.valueOfIgnoreCase(atom.getType_symbol());
  		}  catch (IllegalArgumentException e) {
  			logger.info("Element {} was not recognised as a BioJava-known element, the element will be represented as the generic element {}", atom.getType_symbol(), Element.R.name());
  		}
  		a.setElement(element);
  
  		return a;
  
  	}
docs: Convert a mmCIF AtomSite object to a BioJava Atom object
  
  @param atom the mmmcif AtomSite record
  @return an Atom