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 
13 extern double lxc37_RD; /* parameter for logarithmic loop
14  energy extrapolation */
15 
16 extern int stack37_RD[NBPAIRS+1][NBPAIRS+1];
17 extern int stackdH_RD[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
18 extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
19 
20 extern int hairpin37_RD[31];
21 extern int hairpindH_RD[31];
22 extern int bulge37_RD[31];
23 extern int bulgedH_RD[31];
24 extern int internal_loop37_RD[31];
25 extern int internal_loopdH_RD[31];
26 extern int internal2_energy_RD;
27 extern int old_mismatch_37_RD[NBPAIRS+1][5][5];
28 extern int mismatchI37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
29 extern int mismatchIdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
30 extern int mismatch1nI37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
31 extern int mismatch23I37_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
32 extern int mismatch1nIdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
33 extern int mismatch23IdH_RD[NBPAIRS+1][5][5]; /* interior loop mismatches */
34 extern int mismatchH37_RD[NBPAIRS+1][5][5]; /* same for hairpins */
35 extern int mismatchM37_RD[NBPAIRS+1][5][5]; /* same for multiloops */
36 extern int mismatchHdH_RD[NBPAIRS+1][5][5]; /* same for hairpins */
37 extern int mismatchMdH_RD[NBPAIRS+1][5][5]; /* same for multiloops */
38 extern int mismatchExt37_RD[NBPAIRS+1][5][5];
39 extern int mismatchExtdH_RD[NBPAIRS+1][5][5];
40 
41 extern int dangle5_37_RD[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
42 extern int dangle3_37_RD[NBPAIRS+1][5]; /* 3' dangle */
43 extern int dangle3_dH_RD[NBPAIRS+1][5]; /* corresponding enthalpies */
44 extern int dangle5_dH_RD[NBPAIRS+1][5];
45 
46 extern int int11_37_RD[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
47 extern int int11_dH_RD[NBPAIRS+1][NBPAIRS+1][5][5];
48 
49 extern int int21_37_RD[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
50 extern int int21_dH_RD[NBPAIRS+1][NBPAIRS+1][5][5][5];
51 
52 extern int int22_37_RD[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
53 extern 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 */
57 extern int ML_BASE37_RD;
58 extern int ML_BASEdH_RD;
59 extern int ML_closing37_RD;
60 extern int ML_closingdH_RD;
61 extern int ML_intern37_RD;
62 extern int ML_interndH_RD;
63 
64 extern int TripleC37_RD;
65 extern int TripleCdH_RD;
66 extern int MultipleCA37_RD;
67 extern int MultipleCAdH_RD;
68 extern int MultipleCB37_RD;
69 extern 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}] } */
73 extern int MAX_NINIO_RD; /* maximum correction */
74 extern int ninio37_RD;
75 extern int niniodH_RD;
76 /* penalty for helices terminated by AU (actually not GC) */
77 extern int TerminalAU37_RD;
78 extern int TerminalAUdH_RD;
79 /* penalty for forming bi-molecular duplex */
80 extern int DuplexInit37_RD;
81 extern int DuplexInitdH_RD;
82 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
83 extern char Tetraloops_RD[]; /* string containing the special tetraloops */
84 extern int Tetraloop37_RD[]; /* Bonus energy for special tetraloops */
85 extern int TetraloopdH_RD[];
86 extern char Triloops_RD[]; /* string containing the special triloops */
87 extern int Triloop37_RD[]; /* Bonus energy for special Triloops */
88 extern int TriloopdH_RD[]; /* Bonus energy for special Triloops */
89 extern char Hexaloops_RD[]; /* string containing the special triloops */
90 extern int Hexaloop37_RD[]; /* Bonus energy for special Triloops */
91 extern int HexaloopdH_RD[]; /* Bonus energy for special Triloops */
92 
93 #endif
#define NBPAIRS
Definition: energy_const.h:24