RNAlib-2.6.3
 
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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
5
6#define MOD_PARAMS_STACK_dG (1 << 0)
7#define MOD_PARAMS_STACK_dH (1 << 1)
8#define MOD_PARAMS_MISMATCH_dG (1 << 2)
9#define MOD_PARAMS_MISMATCH_dH (1 << 3)
10#define MOD_PARAMS_TERMINAL_dG (1 << 4)
11#define MOD_PARAMS_TERMINAL_dH (1 << 5)
12#define MOD_PARAMS_DANGLES_dG (1 << 6)
13#define MOD_PARAMS_DANGLES_dH (1 << 7)
14
15/*
16 #define DEBUG
17 */
18#define MAX_ALPHABET (6)
19#define MAX_PAIRS (NBPAIRS + 1 + 25)
20
21
22/* a container to store the data read from a json parameter file */
24 unsigned int available;
25
26 char *name;
27 char one_letter_code;
28 char unmodified;
29 char fallback;
30 char pairing_partners[7];
31 unsigned int pairing_partners_encoding[7];
32 unsigned int unmodified_encoding;
33 unsigned int fallback_encoding;
34
35 size_t num_ptypes;
36 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
37
38 int stack_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
39 int stack_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
40
41 int dangle5_dG[MAX_PAIRS][MAX_ALPHABET];
42 int dangle5_dH[MAX_PAIRS][MAX_ALPHABET];
43 int dangle3_dG[MAX_PAIRS][MAX_ALPHABET];
44 int dangle3_dH[MAX_PAIRS][MAX_ALPHABET];
45
46 int mismatch_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
47 int mismatch_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
48
49 int terminal_dG[MAX_PAIRS];
50 int terminal_dH[MAX_PAIRS];
51};
52
53/* the actual data structure passed around while evaluating */
54typedef struct {
55 short *enc;
56
57 size_t strands;
58 vrna_array(unsigned int *) modification_sites;
59
60 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
61
62 int stack_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
63
64 int dangle5_diff[MAX_PAIRS][MAX_ALPHABET];
65 int dangle3_diff[MAX_PAIRS][MAX_ALPHABET];
66
67 int mismatch_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
68
69 int terminal_diff[MAX_PAIRS];
71
72
73#endif
A macro-based dynamic array implementation.
#define vrna_array(Type)
Define an array.
Definition array.h:99
Definition sc_cb_intern.h:54
Definition sc_cb_intern.h:23