ClassName = Alphabet
Name = pdb_atoms

// The single-letter codes are not really intended for use.
// The short names (abbreviations) are the standard PDB codes for the atoms.

NormalChars = 	NABG12PQSD34UV890TE567WXYRZIJMHLKF$%OC@
Wildcard = ! CANO@
Wildcard = * G1PQS

CharName = 	!	BACK	backbone_atom
CharName = 	*	GAMMA	gamma_for_chi1

CharName=	C	C	carboxyl_carbon
CharName=	A	CA	alpha_carbon
CharName=	B	CB	beta_carbon
CharName=	G	CG	gamma_carbon
CharName=	1	CG1	gamma1_carbon
CharName=	2	CG2	gamma2_carbon
CharName=	D	CD	delta_carbon
CharName=	3	CD1	delta1_carbon
CharName=	4	CD2	delta2_carbon
CharName=	E	CE	epsilon_carbon
CharName=	5	CE1	epsilon1_carbon
CharName=	6	CE2	epsilon2_carbon
CharName=	7	CE3	epsilon3_carbon
CharName=	Z	CZ	zeta_carbon
CharName=	I	CZ2	zeta2_carbon
CharName=	J	CZ3	zeta3_carbon
CharName=	H	CH2	eta_carbon
CharName=	N	N	amide_nitrogen
CharName=	U	ND1	delta1_nitrogen
CharName=	V	ND2	delta2_nitrogen
CharName=	W	NE	epsilon_nitrogen
CharName=	X	NE1	epsilon1_nitrogen
CharName=	Y	NE2	epsilon2_nitrogen
CharName=	M	NZ	zeta_nitrogen
CharName=	L	NH1	eta1_nitrogren
CharName=	K	NH2	eta2_nitrogen
CharName=	O	O	carboxyl_oxygen
CharName=	P	OG	gamma_oxygen
CharName=	Q	OG1	gamma1_oxygen
CharName=	8	OD1	delta1_oxygen
CharName=	9	OD2	delta2_oxygen
CharName=	0	OE1	epsilon1_oxygen
CharName=	R	OE2	epsilon2_oxygen
CharName=	F	OH	eta_oxygen
CharName=	S	SG	gamma_sulphur
CharName=	T	SD	delta_sulphur

// non-standard atoms
CharName=	@	OXT	terminal_oxygen
CharName=	$	UNK	unknown_atom
CharName=	%	CH3	methyl_group

// possible aliases that are not definable in the standard alphabet
//	R	OE	epsilon_oxygen	(alias for OE1)
// 		AD1	OD1 or ND1
//		AD2	OD2 or ND2
//		AE1 	OE1 or NE1
//		AE2	OE2 or NE2

// hydrogen atoms NOT included in this alphabet---there are over 50 of them

EndClassName= Alphabet