05 May 2004 Sol Katzman

See also the README in the "ang" directory, which gives the background
for the "bys" alphabet. "bys" differs from "ang" by the inclusion of
the "C" code, which corresponds to a cis-conformation of the omega angle
preceding the residue being encoded. (Note that IUPAC defines omega as
the angle following a residue, which is not useful for associating a
C code with a Proline residue.)

The "bys" directory contains networks, scripts, and quality reports
for neural nets attempting to predict the secondary structure defined
by partitioning phi/psi space according to a scheme devised by
Bystroff in the HMMSTR paper.  Each phi/psi angle maps to the closest
of the following points, with "C" overriding the phi/psi assignment.

// our             Bystroff's      Andy      center	center
// name            name            Karplus   phi	psi
// H               H               alpha_R    -61.91	 -45.20
// E               E               beta_S    -132.89	 142.43
// P               B               beta_P     -70.58	 147.22
// G               G               delta_R   -109.78	  20.88
// Y               e               epsilon'  -165.00	 175.00
// N               b               gamma'     -85.03	  72.26
// L               L               alpha_L     55.88	  38.62
// T               l               delta_L     85.82	  -0.03
// D               d               zeta      -135.03	  77.26
// S               x               epsilon     80.00	-170.00
// C						cis peptide