code: public Atom[] getAlignmentAtoms(Structure s) {
  		String[] atomNames = params.getUsedAtomNames();
  		return StructureTools.getAtomArray(s, atomNames);
  	}
docs: Returns the atoms that are being used for the alignment. (E.g. Calpha
  only, etc.)
  
  @param s
  @return an array of Atoms objects