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 8 #include <ViennaRNA/params/constants.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 19 extern int hairpin37[31]; 20 extern int hairpindH[31]; 21 extern int bulge37[31]; 22 extern int bulgedH[31]; 23 extern int internal_loop37[31]; 24 extern int internal_loopdH[31]; 25 extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 26 extern int mismatchIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 27 extern int mismatch1nI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 28 extern int mismatch23I37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 29 extern int mismatch1nIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 30 extern int mismatch23IdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 31 extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */ 32 extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */ 33 extern int mismatchHdH[NBPAIRS+1][5][5]; /* same for hairpins */ 34 extern int mismatchMdH[NBPAIRS+1][5][5]; /* same for multiloops */ 35 extern int mismatchExt37[NBPAIRS+1][5][5]; 36 extern int mismatchExtdH[NBPAIRS+1][5][5]; 37 38 extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */ 39 extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */ 40 extern int dangle3_dH[NBPAIRS+1][5]; /* corresponding enthalpies */ 41 extern int dangle5_dH[NBPAIRS+1][5]; 42 43 extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */ 44 extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5]; 45 46 extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */ 47 extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5]; 48 49 extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */ 50 extern 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 */ 54 extern int ML_BASE37; 55 extern int ML_BASEdH; 56 extern int ML_closing37; 57 extern int ML_closingdH; 58 extern int ML_intern37; 59 extern int ML_interndH; 60 61 extern int TripleC37; 62 extern int TripleCdH; 63 extern int MultipleCA37; 64 extern int MultipleCAdH; 65 extern int MultipleCB37; 66 extern 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}] } */ 70 extern int MAX_NINIO; /* maximum correction */ 71 extern int ninio37; 72 extern int niniodH; 73 /* penalty for helices terminated by AU (actually not GC) */ 74 extern int TerminalAU37; 75 extern int TerminalAUdH; 76 /* penalty for forming bi-molecular duplex */ 77 extern int DuplexInit37; 78 extern int DuplexInitdH; 79 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */ 80 extern char Tetraloops[281]; /* string containing the special tetraloops */ 81 extern int Tetraloop37[40]; /* Bonus energy for special tetraloops */ 82 extern int TetraloopdH[40]; 83 extern char Triloops[241]; /* string containing the special triloops */ 84 extern int Triloop37[40]; /* Bonus energy for special Triloops */ 85 extern int TriloopdH[40]; /* Bonus energy for special Triloops */ 86 extern char Hexaloops[361]; /* string containing the special triloops */ 87 extern int Hexaloop37[40]; /* Bonus energy for special Triloops */ 88 extern int HexaloopdH[40]; /* Bonus energy for special Triloops */ 89 90 extern int GQuadAlpha37; 91 extern int GQuadAlphadH; 92 extern int GQuadBeta37; 93 extern int GQuadBetadH; 94 extern int GQuadLayerMismatch37; /* penalty per incompatible gquad layer in a sub-alignment (applied twice for inner layers) */ 95 extern int GQuadLayerMismatchH; 96 extern int GQuadLayerMismatchMax; /* maximum number of mismatching sequences in the alignment when gquad should be formed */ 97 98 extern double Tmeasure; /* temperature of param measurements */ 99 100 #endif 101