RNAlib-2.1.9h
energy_par_D.h
1/*
2 prototypes for energy_par.c
3*/
4
5#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_D_H__
6#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_D_H__
7
8#include "energy_const.h"
9
10#define PUBLIC
11
12
13extern double lxc37_D; /* parameter for logarithmic loop
14 energy extrapolation */
15
16extern int stack37_D[NBPAIRS+1][NBPAIRS+1];
17extern int stackdH_D[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
18extern int entropies_D[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
19
20extern int hairpin37_D[31];
21extern int hairpindH_D[31];
22extern int bulge37_D[31];
23extern int bulgedH_D[31];
24extern int internal_loop37_D[31];
25extern int internal_loopdH_D[31];
26extern int internal2_energy_D;
27extern int old_mismatch_37_D[NBPAIRS+1][5][5];
28extern int mismatchI37_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
29extern int mismatchIdH_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
30extern int mismatch1nI37_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
31extern int mismatch23I37_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
32extern int mismatch1nIdH_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
33extern int mismatch23IdH_D[NBPAIRS+1][5][5]; /* interior loop mismatches */
34extern int mismatchH37_D[NBPAIRS+1][5][5]; /* same for hairpins */
35extern int mismatchM37_D[NBPAIRS+1][5][5]; /* same for multiloops */
36extern int mismatchHdH_D[NBPAIRS+1][5][5]; /* same for hairpins */
37extern int mismatchMdH_D[NBPAIRS+1][5][5]; /* same for multiloops */
38extern int mismatchExt37_D[NBPAIRS+1][5][5];
39extern int mismatchExtdH_D[NBPAIRS+1][5][5];
40
41extern int dangle5_37_D[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
42extern int dangle3_37_D[NBPAIRS+1][5]; /* 3' dangle */
43extern int dangle3_dH_D[NBPAIRS+1][5]; /* corresponding enthalpies */
44extern int dangle5_dH_D[NBPAIRS+1][5];
45
46extern int int11_37_D[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
47extern int int11_dH_D[NBPAIRS+1][NBPAIRS+1][5][5];
48
49extern int int21_37_D[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
50extern int int21_dH_D[NBPAIRS+1][NBPAIRS+1][5][5][5];
51
52extern int int22_37_D[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
53extern int int22_dH_D[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
54
55/* constants for linearly destabilizing contributions for multi-loops
56 F = ML_closing + ML_intern*(k-1) + ML_BASE*u */
57extern int ML_BASE37_D;
58extern int ML_BASEdH_D;
59extern int ML_closing37_D;
60extern int ML_closingdH_D;
61extern int ML_intern37_D;
62extern int ML_interndH_D;
63
64extern int DuplexInit37_D;
65extern int DuplexInitdH_D;
66
67extern int TripleC37_D;
68extern int TripleCdH_D;
69extern int MultipleCA37_D;
70extern int MultipleCAdH_D;
71extern int MultipleCB37_D;
72extern int MultipleCBdH_D;
73
74/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
75/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
76extern int MAX_NINIO_D; /* maximum correction */
77extern int ninio37_D;
78extern int niniodH_D;
79/* penalty for helices terminated by AU (actually not GC) */
80extern int TerminalAU37_D;
81extern int TerminalAUdH_D;
82/* penalty for forming bi-molecular duplex */
83extern int DuplexInit37_D;
84extern int DuplexInitdH_D;
85/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
86extern char Tetraloops_D[]; /* string containing the special tetraloops */
87extern int Tetraloop37_D[]; /* Bonus energy for special tetraloops */
88extern int TetraloopdH_D[];
89extern char Triloops_D[]; /* string containing the special triloops */
90extern int Triloop37_D[]; /* Bonus energy for special Triloops */
91extern int TriloopdH_D[]; /* Bonus energy for special Triloops */
92extern char Hexaloops_D[]; /* string containing the special triloops */
93extern int Hexaloop37_D[]; /* Bonus energy for special Triloops */
94extern int HexaloopdH_D[]; /* Bonus energy for special Triloops */
95
96#endif
#define NBPAIRS
Definition energy_const.h:24