code: public static List<Atom[]> findAtomLinkages(final Group group1,
  			final Group group2, final boolean ignoreNCLinkage,
  			final double bondLengthTolerance) {
  		return findAtomLinkages(group1, group2,
  				null, null, ignoreNCLinkage, bondLengthTolerance);
  	}
docs: Find linkages between two groups within tolerance of bond length,
  from potential atoms.
  @param group1 the first {@link Group}.
  @param group2 the second {@link Group}.
  @param ignoreNCLinkage true to ignore all N-C linkages
  @param bondLengthTolerance bond length error tolerance.
  @return a list, each element of which is an array of two Atoms that form bond
  between each other.