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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
13 extern double lxc37; /* parameter for logarithmic loop
14 energy extrapolation */
15
16 extern int stack37[NBPAIRS+1][NBPAIRS+1];
17 extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */
18 extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */
19
20 extern int hairpin37[31];
21 extern int hairpindH[31];
22 extern int bulge37[31];
23 extern int bulgedH[31];
24 extern int internal_loop37[31];
25 extern int internal_loopdH[31];
26 extern int internal2_energy;
27 extern int old_mismatch_37[NBPAIRS+1][5][5];
28 extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
29 extern int mismatchIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
30 extern int mismatch1nI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
31 extern int mismatch23I37[NBPAIRS+1][5][5]; /* interior loop mismatches */
32 extern int mismatch1nIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
33 extern int mismatch23IdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
34 extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */
35 extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */
36 extern int mismatchHdH[NBPAIRS+1][5][5]; /* same for hairpins */
37 extern int mismatchMdH[NBPAIRS+1][5][5]; /* same for multiloops */
38 extern int mismatchExt37[NBPAIRS+1][5][5];
39 extern int mismatchExtdH[NBPAIRS+1][5][5];
40
41 extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
42 extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */
43 extern int dangle3_dH[NBPAIRS+1][5]; /* corresponding enthalpies */
44 extern int dangle5_dH[NBPAIRS+1][5];
45
46 extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
47 extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];
48
49 extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
50 extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];
51
52 extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
53 extern 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 */
57 extern int ML_BASE37;
58 extern int ML_BASEdH;
59 extern int ML_closing37;
60 extern int ML_closingdH;
61 extern int ML_intern37;
62 extern int ML_interndH;
63
64 extern int TripleC37;
65 extern int TripleCdH;
66 extern int MultipleCA37;
67 extern int MultipleCAdH;
68 extern int MultipleCB37;
69 extern 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}] } */
73 extern int MAX_NINIO; /* maximum correction */
74 extern int ninio37;
75 extern int niniodH;
76 /* penalty for helices terminated by AU (actually not GC) */
77 extern int TerminalAU37;
78 extern int TerminalAUdH;
79 /* penalty for forming bi-molecular duplex */
80 extern int DuplexInit37;
81 extern int DuplexInitdH;
82 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
83 extern char Tetraloops[]; /* string containing the special tetraloops */
84 extern int Tetraloop37[]; /* Bonus energy for special tetraloops */
85 extern int TetraloopdH[];
86 extern char Triloops[]; /* string containing the special triloops */
87 extern int Triloop37[]; /* Bonus energy for special Triloops */
88 extern int TriloopdH[]; /* Bonus energy for special Triloops */
89 extern char Hexaloops[]; /* string containing the special triloops */
90 extern int Hexaloop37[]; /* Bonus energy for special Triloops */
91 extern int HexaloopdH[]; /* Bonus energy for special Triloops */
92
93 extern int GQuadAlpha37;
94 extern int GQuadAlphadH;
95 extern int GQuadBeta37;
96 extern int GQuadBetadH;
97
98 extern double Tmeasure; /* temperature of param measurements */
99
100 #endif