The directory 
	/projects/compbio/lib/alphabet
contains definitions of various alphabets that are usable with the
Alphabet class in the "ultimate" library.

The alphabet files are
			contains
	std.alphabet	AA, ExtAA, Nucleic, DNA, RNA, ExtDNA
			all the standard nucleic acid and amino acid alphabets
	
	ExtAA.alphabet	ExtAA
			most popular amino acid alphabet
	
	ExtDNA.alphabet	ExtDNA
			most popular nucleic acid alphabet
			
	DSSP.alphabet	DSSP, EHL, EHTL
			secondary-structure alphabets

	DMI.alphabet	DMI, DMIS
			transition alphabets

	RBK.alphabet	RBK
			remove-borderline-keep

	pdb_atoms.alphabet	pdb_atoms
			non-hydrogen atoms in PDB files
			(single letter codes not intended for use---abbreviations
			are the PDB codes)
	
	OneTwoThree.alphabet	OneTwoThree
			alphabet for homework exercises: letters 1,2,3

	two-spot-burial.alphabet	
			burial alphabets for two-spot burial (put a
			"count" spot for each residue, then count them in
			spheres centered at the "center" spot)
			near-backbone-9.5-7
			near-backbone-9.5-10
			near-backbone-9.5-11
			way-back-8.9-7
			way-back-8.9-11

Other files:
	aa.atoms	A file containing a prototype of each amino acid,
			in the "ChainsResiduesAndAtoms" format.
	
	aa.bonds	A file containing the known bonds internal to
			amino acid residues.