RNAlib-2.1.9h
energy_par_RD.h
1/*
2 prototypes for energy_par.c
3*/
4
5#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_RD_H__
6#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_RD_H__
7
8#include "energy_const.h"
9
10#define PUBLIC
11
12
13extern double lxc37_RD; /* parameter for logarithmic loop
14 energy extrapolation */
15
16extern int stack37_RD[NBPAIRS+1][NBPAIRS+1];
17extern int stackdH_RD[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
18extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
19
20extern int hairpin37_RD[31];
21extern int hairpindH_RD[31];
22extern int bulge37_RD[31];
23extern int bulgedH_RD[31];
24extern int internal_loop37_RD[31];
25extern int internal_loopdH_RD[31];
26extern int internal2_energy_RD;
27extern int old_mismatch_37_RD[NBPAIRS+1][5][5];
28extern int mismatchI37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
29extern int mismatchIdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
30extern int mismatch1nI37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
31extern int mismatch23I37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
32extern int mismatch1nIdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
33extern int mismatch23IdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
34extern int mismatchH37_RD[NBPAIRS+1][5][5]; /* same for hairpins */
35extern int mismatchM37_RD[NBPAIRS+1][5][5]; /* same for multiloops */
36extern int mismatchHdH_RD[NBPAIRS+1][5][5]; /* same for hairpins */
37extern int mismatchMdH_RD[NBPAIRS+1][5][5]; /* same for multiloops */
38extern int mismatchExt37_RD[NBPAIRS+1][5][5];
39extern int mismatchExtdH_RD[NBPAIRS+1][5][5];
40
41extern int dangle5_37_RD[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
42extern int dangle3_37_RD[NBPAIRS+1][5]; /* 3' dangle */
43extern int dangle3_dH_RD[NBPAIRS+1][5]; /* corresponding enthalpies */
44extern int dangle5_dH_RD[NBPAIRS+1][5];
45
46extern int int11_37_RD[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
47extern int int11_dH_RD[NBPAIRS+1][NBPAIRS+1][5][5];
48
49extern int int21_37_RD[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
50extern int int21_dH_RD[NBPAIRS+1][NBPAIRS+1][5][5][5];
51
52extern int int22_37_RD[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
53extern int int22_dH_RD[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_RD;
58extern int ML_BASEdH_RD;
59extern int ML_closing37_RD;
60extern int ML_closingdH_RD;
61extern int ML_intern37_RD;
62extern int ML_interndH_RD;
63
64extern int TripleC37_RD;
65extern int TripleCdH_RD;
66extern int MultipleCA37_RD;
67extern int MultipleCAdH_RD;
68extern int MultipleCB37_RD;
69extern int MultipleCBdH_RD;
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_RD; /* maximum correction */
74extern int ninio37_RD;
75extern int niniodH_RD;
76/* penalty for helices terminated by AU (actually not GC) */
77extern int TerminalAU37_RD;
78extern int TerminalAUdH_RD;
79/* penalty for forming bi-molecular duplex */
80extern int DuplexInit37_RD;
81extern int DuplexInitdH_RD;
82/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
83extern char Tetraloops_RD[]; /* string containing the special tetraloops */
84extern int Tetraloop37_RD[]; /* Bonus energy for special tetraloops */
85extern int TetraloopdH_RD[];
86extern char Triloops_RD[]; /* string containing the special triloops */
87extern int Triloop37_RD[]; /* Bonus energy for special Triloops */
88extern int TriloopdH_RD[]; /* Bonus energy for special Triloops */
89extern char Hexaloops_RD[]; /* string containing the special triloops */
90extern int Hexaloop37_RD[]; /* Bonus energy for special Triloops */
91extern int HexaloopdH_RD[]; /* Bonus energy for special Triloops */
92
93#endif
#define NBPAIRS
Definition energy_const.h:24