BioJava:CookBook:PDB:ligands

From BioJava

         //get a structure
         Structure struct = structure;
         //get the non-water HETATOM groups in the structure
         List<Group> hets = struct.getHetGroups();
            for (Group group : hets) {
                System.out.println(group);
                //for every Group in the list find all other groups in the structure within 4.00 Angstrom, not including waters
                List<Group> fourAngstromShell = StructureTools.getGroupsWithinShell(struct, group, 4.00, false);
                System.out.println("Groups within 4.00 Angstroms of " + group + ":");
                for (Group fourAngstromgroup : fourAngstromShell) {
                    System.out.println(fourAngstromgroup);
 
                }
                //find the inter-molecular bonds between a group and the surrounding groups 
                for (Bond bond : StructureTools.findBonds(group, fourAngstromShell)) {
                        System.out.println(bond);
                }
            }

n.b. StructureTools.findBonds() is currently under development and will not give chemically correct answers. However, it will give very quick and dirty approximations based on distances.