------------------------------------------------------------------------
Since v0.04
DATE: 2007-02-20
Found a bug in the way Numpy was returning values from its' det
function.  It was returning something that was not casting correctly to
Python's internal types.  For example, the determinant of an orthonormal
matrix must be +/- 1.0 -- and hence the product of two orthonormal
matrices must also be +/- 1.0 -- but here were the test results from
Numpy:
	Reflect => -1.0
		Does reflect equal 1.0 => False
	Reflect => -1.0
		Does reflect equal -1.0 =>False

The second case is obviously wrong, and the program was never properly
detecting reflections.  The fix is:

	reflect = float(str(float(numpy.linalg.det(V) * numpy.linalg.det(Wt))))
	
	if reflect == -1.0:
		S[-1] = -S[-1]
		V[:,-1] = -V[:,-1]

A BIG thanks to Dan Kulp for finding the error!

------------------------------------------------------------------------
Since v0.03
DATE: 2007-02-01
Found a small bug with calculating scores.  Alignments should, in
general be of lower RMSD and longer.

------------------------------------------------------------------------
Since v0.02
DATE: 2007-01-31
Found a small bug in sequencing.  Fixed it.

------------------------------------------------------------------------
Since v0.01
DATE: 2007-01-25

CEAlign has the semantic, and syntactic formalism of

 cealign MASTER, TARGET

where a post-condition of the algorithm is that the coordinates of the
'''MASTER''' protein are unchanged.  This allows for easier
multi-protein alignments.  For example,

 cealign 1AUE, 1BZ4
 cealign 1AUE, 1B68
 cealign 1AUE, 1A7V
 cealign 1AUE, 1CPR

will superimpose all the TARGETS onto the MASTER.

