code: public static AtomContactSet getAtomsInContact(Chain chain, double cutoff) {
  		return getAtomsInContact(chain, (String[]) null, cutoff);
  	}
docs: Returns the set of intra-chain contacts for the given chain for all non-H
  atoms of non-hetatoms, 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