RNAlib-2.6.1
 
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sc_cb_intern.h
1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H
3
4#define MOD_PARAMS_STACK_dG (1 << 0)
5#define MOD_PARAMS_STACK_dH (1 << 1)
6#define MOD_PARAMS_MISMATCH_dG (1 << 2)
7#define MOD_PARAMS_MISMATCH_dH (1 << 3)
8#define MOD_PARAMS_TERMINAL_dG (1 << 4)
9#define MOD_PARAMS_TERMINAL_dH (1 << 5)
10#define MOD_PARAMS_DANGLES_dG (1 << 6)
11#define MOD_PARAMS_DANGLES_dH (1 << 7)
12
13/*
14 #define DEBUG
15 */
16#define MAX_ALPHABET (6)
17#define MAX_PAIRS (NBPAIRS + 1 + 25)
18
19
20/* a container to store the data read from a json parameter file */
22 unsigned int available;
23
24 char *name;
25 char one_letter_code;
26 char unmodified;
27 char fallback;
28 char pairing_partners[7];
29 unsigned int pairing_partners_encoding[7];
30 unsigned int unmodified_encoding;
31 unsigned int fallback_encoding;
32
33 size_t num_ptypes;
34 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
35
36 int stack_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
37 int stack_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
38
39 int dangle5_dG[MAX_PAIRS][MAX_ALPHABET];
40 int dangle5_dH[MAX_PAIRS][MAX_ALPHABET];
41 int dangle3_dG[MAX_PAIRS][MAX_ALPHABET];
42 int dangle3_dH[MAX_PAIRS][MAX_ALPHABET];
43
44 int mismatch_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
45 int mismatch_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
46
47 int terminal_dG[MAX_PAIRS];
48 int terminal_dH[MAX_PAIRS];
49};
50
51/* the actual data structure passed around while evaluating */
52typedef struct {
53 short *enc;
54 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
55
56 int stack_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
57
58 int dangle5_diff[MAX_PAIRS][MAX_ALPHABET];
59 int dangle3_diff[MAX_PAIRS][MAX_ALPHABET];
60
61 int mismatch_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
62
63 int terminal_diff[MAX_PAIRS];
65
66
67#endif
Definition sc_cb_intern.h:52
Definition sc_cb_intern.h:21