2 Current free energy parameters are summarized in:
4 D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner
5 "Expanded sequence dependence of thermodynamic parameters improves
6 prediction of RNA secondary structure"
7 JMB, 288, pp 911-940, 1999
11 A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker
12 "Coaxial stckaing of helices enhances binding of oligoribonucleotides.."
13 PNAS, 91, pp 9218-9222, 1994
15 D.H. Turner, N. Sugimoto, and S.M. Freier.
16 "RNA Structure Prediction",
17 Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.
19 John A.Jaeger, Douglas H.Turner, and Michael Zuker.
20 "Improved predictions of secondary structures for RNA",
21 PNAS, 86, 7706-7710, October 1989.
23 L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner
24 "Nearest-Neughbor Parameters for GU Mismatches...."
25 Biochemistry 1991, 30 11124-11132
27 A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner
28 "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."
29 Biochemistry 1991, 30, 6428--6435
34 #ifndef ENERGY_PARAM_H
35 #define ENERGY_PARAM_H
38 #include <cstdlib> // by katoh
48 static const double lxc37; /* parameter for logarithmic loop
49 energy extrapolation */
50 static const int stack37[8][8];
51 static const int enthalpies[8][8];
52 static const int oldhairpin37[31];
53 static const int hairpin37[31];
54 static const int oldbulge37[31];
55 static const int bulge37[31];
56 static const int oldinternal_loop37[31];
57 static const int internal_loop37[31];
58 static const int mismatchI37[8][5][5];
59 static const int mismatchH37[8][5][5];
60 static const int mism_H[8][5][5];
61 static const int dangle5_37[8][5];
62 static const int dangle3_37[8][5];
63 static const int dangle3_H[8][5];
64 static const int dangle5_H[8][5];
65 static const int ML_BASE37;
66 static const int ML_closing37;
67 static const int ML_intern37;
68 static const int MAX_NINIO;
69 static const int F_ninio37[5];
70 static const char Tetraloops[1400];
71 static const char Tetrastrings[30][7];
72 static const int TETRA_ENERGY37[200];
73 static const int TETRA_ENTH37;
74 static const int TerminalAU;
75 static const int DuplexInit;
77 static const int int11_37[8][8][5][5];
78 static const int int11_H[8][8][5][5];
79 static const int int21_37[8][8][5][5][5];
80 static const int int21_H[8][8][5][5][5];
81 static const int int22_37[8][8][5][5][5][5];
82 static const int int22_H[8][8][5][5][5][5];
84 int convertPairType(int type);
85 int convertBaseType(int type);
86 int convertLeftType(int type);
87 int convertRightType(int type);
92 int getDangle5(int i, int j);
93 int getDangle3(int i, int j);
94 int getHairpin(int i);
95 int getInternalLoop(int i);
97 const char *getTetraLoop(int i);
98 int getTetraLoopEnergy(int i);
99 int getStack(int i, int j);
100 int getTstackH(int i, int j);
101 int getTstackI(int i, int j);
102 int getInt11(int i, int j, int k);
103 int getInt21(int i, int j, int k, int l);
104 int getInt22(int i, int j, int k, int l);