code: private void formBonds() {
  
  		BondMaker maker = new BondMaker(structure, params);
  
  		// LINK records should be preserved, they are the way that
  		// inter-residue bonds are created for ligands such as trisaccharides, unusual polymers.
  		// The analogy in mmCIF is the _struct_conn record.
  		for (LinkRecord linkRecord : linkRecords) {
  			maker.formLinkRecordBond(linkRecord);
  		}
  
  		maker.formDisulfideBonds(ssbonds);
  
  		maker.makeBonds();
  	}
docs: Handles creation of all bonds. Looks at LINK records, SSBOND (Disulfide
  bonds), peptide bonds, and intra-residue bonds.
  <p>
  Note: the current implementation only looks at the first model of each
  structure. This may need to be fixed in the future.