code: public static AtomContactSet getRepresentativeAtomsInContact(Chain chain,
  			double cutoff) {
  		Grid grid = new Grid(cutoff);
  
  		Atom[] atoms = getRepresentativeAtomArray(chain);
  
  		grid.addAtoms(atoms);
  
  		return grid.getAtomContacts();
  	}
docs: Returns the set of intra-chain contacts for the given chain for C-alpha
  or C3' atoms (including non-standard aminoacids appearing as HETATM
  groups), i.e. the contact map. Uses a geometric hashing algorithm that
  speeds up the calculation without need of full distance matrix.
  
  @param chain
  @param cutoff
  @return
  @since Biojava 4.1.0