RNAlib-2.0.5
|
00001 /* 00002 prototypes for energy_par.c 00003 */ 00004 00005 #ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__ 00006 #define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__ 00007 00008 #include "energy_const.h" 00009 00010 #define PUBLIC 00011 00012 00013 extern double lxc37; /* parameter for logarithmic loop 00014 energy extrapolation */ 00015 00016 extern int stack37[NBPAIRS+1][NBPAIRS+1]; 00017 extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */ 00018 extern int entropies[NBPAIRS+1][NBPAIRS+1]; /* not used anymore */ 00019 00020 extern int hairpin37[31]; 00021 extern int hairpindH[31]; 00022 extern int bulge37[31]; 00023 extern int bulgedH[31]; 00024 extern int internal_loop37[31]; 00025 extern int internal_loopdH[31]; 00026 extern int internal2_energy; 00027 extern int old_mismatch_37[NBPAIRS+1][5][5]; 00028 extern int mismatchI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00029 extern int mismatchIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00030 extern int mismatch1nI37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00031 extern int mismatch23I37[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00032 extern int mismatch1nIdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00033 extern int mismatch23IdH[NBPAIRS+1][5][5]; /* interior loop mismatches */ 00034 extern int mismatchH37[NBPAIRS+1][5][5]; /* same for hairpins */ 00035 extern int mismatchM37[NBPAIRS+1][5][5]; /* same for multiloops */ 00036 extern int mismatchHdH[NBPAIRS+1][5][5]; /* same for hairpins */ 00037 extern int mismatchMdH[NBPAIRS+1][5][5]; /* same for multiloops */ 00038 extern int mismatchExt37[NBPAIRS+1][5][5]; 00039 extern int mismatchExtdH[NBPAIRS+1][5][5]; 00040 00041 extern int dangle5_37[NBPAIRS+1][5]; /* 5' dangle exterior of pair */ 00042 extern int dangle3_37[NBPAIRS+1][5]; /* 3' dangle */ 00043 extern int dangle3_dH[NBPAIRS+1][5]; /* corresponding enthalpies */ 00044 extern int dangle5_dH[NBPAIRS+1][5]; 00045 00046 extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */ 00047 extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5]; 00048 00049 extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */ 00050 extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5]; 00051 00052 extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */ 00053 extern int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; 00054 00055 /* constants for linearly destabilizing contributions for multi-loops 00056 F = ML_closing + ML_intern*(k-1) + ML_BASE*u */ 00057 extern int ML_BASE37; 00058 extern int ML_BASEdH; 00059 extern int ML_closing37; 00060 extern int ML_closingdH; 00061 extern int ML_intern37; 00062 extern int ML_interndH; 00063 00064 extern int TripleC37; 00065 extern int TripleCdH; 00066 extern int MultipleCA37; 00067 extern int MultipleCAdH; 00068 extern int MultipleCB37; 00069 extern int MultipleCBdH; 00070 00071 /* Ninio-correction for asymmetric internal loops with branches n1 and n2 */ 00072 /* ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */ 00073 extern int MAX_NINIO; /* maximum correction */ 00074 extern int ninio37; 00075 extern int niniodH; 00076 /* penalty for helices terminated by AU (actually not GC) */ 00077 extern int TerminalAU37; 00078 extern int TerminalAUdH; 00079 /* penalty for forming bi-molecular duplex */ 00080 extern int DuplexInit37; 00081 extern int DuplexInitdH; 00082 /* stabilizing contribution due to special hairpins of size 4 (tetraloops) */ 00083 extern char Tetraloops[]; /* string containing the special tetraloops */ 00084 extern int Tetraloop37[]; /* Bonus energy for special tetraloops */ 00085 extern int TetraloopdH[]; 00086 extern char Triloops[]; /* string containing the special triloops */ 00087 extern int Triloop37[]; /* Bonus energy for special Triloops */ 00088 extern int TriloopdH[]; /* Bonus energy for special Triloops */ 00089 extern char Hexaloops[]; /* string containing the special triloops */ 00090 extern int Hexaloop37[]; /* Bonus energy for special Triloops */ 00091 extern int HexaloopdH[]; /* Bonus energy for special Triloops */ 00092 00093 extern double Tmeasure; /* temperature of param measurements */ 00094 00095 #endif