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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy_par.h

    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 int GQuadAlpha37;
    00094 extern int GQuadAlphadH;
    00095 extern int GQuadBeta37;
    00096 extern int GQuadBetadH;
    00097
    00098 extern double Tmeasure;       /* temperature of param measurements */
    00099
    00100 #endif