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/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* aabet.h: Definitions for amino acids */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef __AABET_H__
#define __AABET_H__
#define AAID_MIN 1 /* Smallest letter value in binary alphabet */
#define AAID_MAX 24 /* Maximum letter value in binary alphabet */
#define AAID_CNT 24 /* Number of letters in alphabet */
#define AAID_NAR (AAID_MAX+1)
#define AAID_IGNORE (AAID_MAX+3)
#define NA AAID_NAR /* Not A residue */
#define EL (NA+1) /* End of Line */
#define ES (NA+2) /* End of Sequence */
#define IC AAID_IGNORE /* Ignore this Character */
#define UNKNOWN_AA_CHR 'X'
#define STOP_AA_CHR '*'
#define GAP_AA_CHR '-'
/* Alpha chars that are not codes are treated as wildcard place holders */
/* (unknown amino acids) */
#define UN 23 /* 23 = 'X' an unknown aa */
EXTERN int aa_atob[1<<CHAR_BIT] /* ASCII-to-binary translation table */
#ifdef INIT
= {
EL,NA,NA,NA,NA,NA,NA,NA,NA,IC,EL,NA,NA,EL,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
IC,NA,NA,NA,NA,NA,NA,NA,NA,NA,24,NA,NA, 0,24,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
ES, 1,21, 5, 4, 7,14, 8, 9,10,UN,12,11,13, 3,UN,
15, 6, 2,16,17,UN,20,18,23,19,22,NA,NA,NA,NA,NA,
ES, 1,21, 5, 4, 7,14, 8, 9,10,UN,12,11,13, 3,UN,
15, 6, 2,16,17,UN,20,18,23,19,22,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA }
#endif
;
/* binary-to-ASCII translation table */
EXTERN char aa_btoa[] INITIAL("-ARNDCQEGHILKMFPSTWYVBZX*");
EXTERN Degen aa_adegen[25]
#ifdef INIT
= {
'-', 1, "-",
'A', 1, "A",
'R', 1, "R",
'N', 1, "N",
'D', 1, "D",
'C', 1, "C",
'Q', 1, "Q",
'E', 1, "E",
'G', 1, "G",
'H', 1, "H",
'I', 1, "I",
'L', 1, "L",
'K', 1, "K",
'M', 1, "M",
'F', 1, "F",
'P', 1, "P",
'S', 1, "S",
'T', 1, "T",
'W', 1, "W",
'Y', 1, "Y",
'V', 1, "V",
'B', 2, "DN",
'Z', 2, "EQ",
'X', 20, "ARNDCQEGHILKMFPSTWYV",
'*', 1, "*"
}
#endif
;
#undef NA
#undef EL
#undef ES
#undef IC
#undef UN
EXTERN double aafq[21]
#ifdef INIT
/* Amino acid residue frequencies used by S. Altschul */
= {0, .081, .057, .045, .054, .015, .039, .061, .068, .022, .057,
.093, .056, .025, .040, .049, .068, .058, .013, .032, .067 }
#endif
;
#endif /* !__AABET_H__ */
/* Change log information follows. */
/*
* Revision 0.52 1993/07/27 20:26:13 billa
* Modified aa_atob so that alphabetic characters that are not codes are
* treated as unknown amino acids for placeholding. Also the IUB code for
* stop, '.', was added. The changes are:
* 'J', 'O', 'U' get the same binary representation as 'X'
* '.' gets the same binary representation as '*'
*
*/
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