1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H
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)
16#define MAX_ALPHABET (6)
17#define MAX_PAIRS (NBPAIRS + 1 + 25)
22 unsigned int available;
27 char pairing_partners[7];
28 unsigned int pairing_partners_encoding[7];
29 unsigned int unmodified_encoding;
32 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
34 int stack_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
35 int stack_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
37 int dangle5_dG[MAX_PAIRS][MAX_ALPHABET];
38 int dangle5_dH[MAX_PAIRS][MAX_ALPHABET];
39 int dangle3_dG[MAX_PAIRS][MAX_ALPHABET];
40 int dangle3_dH[MAX_PAIRS][MAX_ALPHABET];
42 int mismatch_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
43 int mismatch_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
45 int terminal_dG[MAX_PAIRS];
46 int terminal_dH[MAX_PAIRS];
52 size_t ptypes[MAX_ALPHABET][MAX_ALPHABET];
54 int stack_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
56 int dangle5_diff[MAX_PAIRS][MAX_ALPHABET];
57 int dangle3_diff[MAX_PAIRS][MAX_ALPHABET];
59 int mismatch_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];
61 int terminal_diff[MAX_PAIRS];
Definition: sc_cb_intern.h:50
Definition: sc_cb_intern.h:21