code: public static AtomContactSet getAtomsCAInContact(Chain chain, double cutoff) {
  		Grid grid = new Grid(cutoff);
  
  		Atom[] atoms = getAtomCAArray(chain);
  
  		grid.addAtoms(atoms);
  
  		return grid.getAtomContacts();
  	}
docs: Returns the set of intra-chain contacts for the given chain for C-alpha
  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. The parsing mode
  {@link FileParsingParameters#setAlignSeqRes(boolean)} needs to be set to
  true for this to work.
  
  @param chain
  @param cutoff
  @return
  @see {@link #getRepresentativeAtomsInContact(Chain, double)}