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();
	}
private void formBonds ( ) { BondMaker maker = new BondMaker ( structure , params ) ; for ( LinkRecord linkRecord : linkRecords ) { maker . formLinkRecordBond ( linkRecord ) ; } maker . formDisulfideBonds ( ssbonds ) ; maker . makeBonds ( ) ; }
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.