RNAlib-2.0.7: H/energy_par.h Source File

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