/** * 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. */ 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(); }