code: public static double getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) throws StructureException {
  		return getTMScore(atomSet1, atomSet2, len1, len2,true);
  	}
docs: Calculate the TM-Score for the superposition.
  
  <em>Normalizes by the <strong>minimum</strong>-length structure (that is, {@code min\{len1,len2\}}).</em>
  
  Atom sets must be pre-rotated.
  
  <p>
  Citation:<br/>
  <i>Zhang Y and Skolnick J (2004). "Scoring function for automated
  assessment of protein structure template quality". Proteins 57: 702 -
  710.</i>
  
  @param atomSet1
  atom array 1
  @param atomSet2
  atom array 2
  @param len1
  The full length of the protein supplying atomSet1
  @param len2
  The full length of the protein supplying atomSet2
  @return The TM-Score
  @throws StructureException