code: public void formLinkRecordBond(LinkRecord linkRecord) {
  		// only work with atoms that aren't alternate locations
  		if (linkRecord.getAltLoc1().equals(" ")
  				|| linkRecord.getAltLoc2().equals(" "))
  			return;
  
  		try {
  			Map<Integer, Atom> a = getAtomFromRecord(linkRecord.getName1(),
  					linkRecord.getAltLoc1(), linkRecord.getResName1(),
  					linkRecord.getChainID1(), linkRecord.getResSeq1(),
  					linkRecord.getiCode1());
  
  			Map<Integer, Atom> b = getAtomFromRecord(linkRecord.getName2(),
  					linkRecord.getAltLoc2(), linkRecord.getResName2(),
  					linkRecord.getChainID2(), linkRecord.getResSeq2(),
  					linkRecord.getiCode2());
  
  			for(int i=0; i<structure.nrModels(); i++){
  				if(a.containsKey(i) && b.containsKey(i)){
  					// TODO determine what the actual bond order of this bond is; for
  					// now, we're assuming they're single bonds
  					if(!a.get(i).equals(b.get(i))){
  						new BondImpl(a.get(i), b.get(i), 1);
  					}
  				}
  			}
  		}catch (StructureException e) {
  			// Note, in Calpha only mode the link atoms may not be present.
  			if (! params.isParseCAOnly()) {
  				logger.warn("Could not find atoms specified in LINK record: {}",linkRecord.toString());
  			} else {
  				logger.debug("Could not find atoms specified in LINK record while parsing in parseCAonly mode.");
  			}
  
  		}
  	}
docs: Creates bond objects from a LinkRecord as parsed from a PDB file
  @param linkRecord