RNAlib-2.5.1
default.h
1/*
2 prototypes for energy_par.c
3*/
4
5#ifndef VIENNA_RNA_PACKAGE_PARAMS_DEFAULT_H
6#define VIENNA_RNA_PACKAGE_PARAMS_DEFAULT_H
7
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 */
18
19extern int hairpin37[31];
20extern int hairpindH[31];
21extern int bulge37[31];
22extern int bulgedH[31];
23extern int internal_loop37[31];
24extern int internal_loopdH[31];
25extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
26extern int mismatchIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
27extern int mismatch1nI37[NBPAIRS+1][5][5]; /* interior loop mismatches */
28extern int mismatch23I37[NBPAIRS+1][5][5]; /* interior loop mismatches */
29extern int mismatch1nIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
30extern int mismatch23IdH[NBPAIRS+1][5][5]; /* interior loop mismatches */
31extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */
32extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */
33extern int mismatchHdH[NBPAIRS+1][5][5]; /* same for hairpins */
34extern int mismatchMdH[NBPAIRS+1][5][5]; /* same for multiloops */
35extern int mismatchExt37[NBPAIRS+1][5][5];
36extern int mismatchExtdH[NBPAIRS+1][5][5];
37
38extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */
39extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */
40extern int dangle3_dH[NBPAIRS+1][5]; /* corresponding enthalpies */
41extern int dangle5_dH[NBPAIRS+1][5];
42
43extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */
44extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];
45
46extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */
47extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];
48
49extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */
50extern int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
51
52/* constants for linearly destabilizing contributions for multi-loops
53 F = ML_closing + ML_intern*(k-1) + ML_BASE*u */
54extern int ML_BASE37;
55extern int ML_BASEdH;
56extern int ML_closing37;
57extern int ML_closingdH;
58extern int ML_intern37;
59extern int ML_interndH;
60
61extern int TripleC37;
62extern int TripleCdH;
63extern int MultipleCA37;
64extern int MultipleCAdH;
65extern int MultipleCB37;
66extern int MultipleCBdH;
67
68/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */
69/* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */
70extern int MAX_NINIO; /* maximum correction */
71extern int ninio37;
72extern int niniodH;
73/* penalty for helices terminated by AU (actually not GC) */
74extern int TerminalAU37;
75extern int TerminalAUdH;
76/* penalty for forming bi-molecular duplex */
77extern int DuplexInit37;
78extern int DuplexInitdH;
79/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */
80extern char Tetraloops[281]; /* string containing the special tetraloops */
81extern int Tetraloop37[40]; /* Bonus energy for special tetraloops */
82extern int TetraloopdH[40];
83extern char Triloops[241]; /* string containing the special triloops */
84extern int Triloop37[40]; /* Bonus energy for special Triloops */
85extern int TriloopdH[40]; /* Bonus energy for special Triloops */
86extern char Hexaloops[361]; /* string containing the special triloops */
87extern int Hexaloop37[40]; /* Bonus energy for special Triloops */
88extern int HexaloopdH[40]; /* Bonus energy for special Triloops */
89
90extern int GQuadAlpha37;
91extern int GQuadAlphadH;
92extern int GQuadBeta37;
93extern int GQuadBetadH;
94extern int GQuadLayerMismatch37; /* penalty per incompatible gquad layer in a sub-alignment (applied twice for inner layers) */
95extern int GQuadLayerMismatchH;
96extern int GQuadLayerMismatchMax; /* maximum number of mismatching sequences in the alignment when gquad should be formed */
97
98extern double Tmeasure; /* temperature of param measurements */
99
100#endif
Energy parameter constants.
#define NBPAIRS
Definition: constants.h:25