RNAlib-2.1.9h
energy_par.h
1/*
2 prototypes for energy_par.c
3*/
4
5#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__
6#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__
7
8#include "energy_const.h"
9
10#define PUBLIC
11
12
13extern double lxc37; /* parameter for logarithmic loop
14 energy extrapolation */
15
16extern int stack37[NBPAIRS+1][NBPAIRS+1];
17extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
18extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
19
20extern int hairpin37[31];
21extern int hairpindH[31];
22extern int bulge37[31];
23extern int bulgedH[31];
24extern int internal_loop37[31];
25extern int internal_loopdH[31];
26extern int internal2_energy;
27extern int old_mismatch_37[NBPAIRS+1][5][5];
28extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
29extern int mismatchIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
30extern int mismatch1nI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
31extern int mismatch23I37[NBPAIRS+1][5][5]; /* interior loop mismatches */
32extern int mismatch1nIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
33extern int mismatch23IdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
34extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */
35extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */
36extern int mismatchHdH[NBPAIRS+1][5][5]; /* same for hairpins */
37extern int mismatchMdH[NBPAIRS+1][5][5]; /* same for multiloops */
38extern int mismatchExt37[NBPAIRS+1][5][5];
39extern int mismatchExtdH[NBPAIRS+1][5][5];
40
41extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
42extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */
43extern int dangle3_dH[NBPAIRS+1][5]; /* corresponding enthalpies */
44extern int dangle5_dH[NBPAIRS+1][5];
45
46extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
47extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];
48
49extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
50extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];
51
52extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
53extern int int22_dH[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;
58extern int ML_BASEdH;
59extern int ML_closing37;
60extern int ML_closingdH;
61extern int ML_intern37;
62extern int ML_interndH;
63
64extern int TripleC37;
65extern int TripleCdH;
66extern int MultipleCA37;
67extern int MultipleCAdH;
68extern int MultipleCB37;
69extern int MultipleCBdH;
70
71/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
72/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
73extern int MAX_NINIO; /* maximum correction */
74extern int ninio37;
75extern int niniodH;
76/* penalty for helices terminated by AU (actually not GC) */
77extern int TerminalAU37;
78extern int TerminalAUdH;
79/* penalty for forming bi-molecular duplex */
80extern int DuplexInit37;
81extern int DuplexInitdH;
82/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
83extern char Tetraloops[]; /* string containing the special tetraloops */
84extern int Tetraloop37[]; /* Bonus energy for special tetraloops */
85extern int TetraloopdH[];
86extern char Triloops[]; /* string containing the special triloops */
87extern int Triloop37[]; /* Bonus energy for special Triloops */
88extern int TriloopdH[]; /* Bonus energy for special Triloops */
89extern char Hexaloops[]; /* string containing the special triloops */
90extern int Hexaloop37[]; /* Bonus energy for special Triloops */
91extern int HexaloopdH[]; /* Bonus energy for special Triloops */
92
93extern int GQuadAlpha37;
94extern int GQuadAlphadH;
95extern int GQuadBeta37;
96extern int GQuadBetadH;
97
98extern double Tmeasure; /* temperature of param measurements */
99
100#include "energy_par_D.h"
101#include "energy_par_RD.h"
102
103#endif
#define NBPAIRS
Definition energy_const.h:24